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
LOC643837	643837	broad.mit.edu	37	1	788350	788351	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:788350_788351insT	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																		---	---	---	---
TTLL10	254173	broad.mit.edu	37	1	1116223	1116223	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1116223delG	uc001acy.2	+	8	889	c.738delG	c.(736-738)CCGfs	p.P246fs	uc001acx.1_5'Flank|TTLL10_uc010nyg.1_Frame_Shift_Del_p.P246fs|TTLL10_uc001acz.1_Frame_Shift_Del_p.P173fs	NM_001130045	NP_001123517	Q6ZVT0	TTL10_HUMAN	tubulin tyrosine ligase-like family, member 10	246	TTL.				protein modification process		ATP binding|tubulin-tyrosine ligase activity			large_intestine(1)	1	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;4.75e-36)|OV - Ovarian serous cystadenocarcinoma(86;5.82e-22)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	1880034	1880036	+	IGR	DEL	TTT	-	-	rs150214777		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1880034_1880036delTTT								TMEM52 (29294 upstream) : KIAA1751 (4716 downstream)																																			---	---	---	---
PRKCZ	5590	broad.mit.edu	37	1	2104535	2104538	+	Intron	DEL	CCAC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2104535_2104538delCCAC	uc001aiq.2	+						PRKCZ_uc001air.2_Intron|PRKCZ_uc010nyw.1_Intron|PRKCZ_uc001ais.2_Intron|PRKCZ_uc009vla.2_Intron|PRKCZ_uc010nyx.1_Intron|PRKCZ_uc001ait.2_Intron	NM_002744	NP_002735			protein kinase C, zeta isoform 1						anti-apoptosis|intracellular signal transduction|negative regulation of insulin receptor signaling pathway|negative regulation of peptidyl-tyrosine phosphorylation|negative regulation of protein complex assembly|peptidyl-serine phosphorylation|platelet activation	endosome	ATP binding|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(2)	6	all_cancers(77;0.000177)|all_epithelial(69;6.41e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.96e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.3e-23)|GBM - Glioblastoma multiforme(42;2.85e-08)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00294)|BRCA - Breast invasive adenocarcinoma(365;0.00493)|STAD - Stomach adenocarcinoma(132;0.00669)|KIRC - Kidney renal clear cell carcinoma(229;0.0411)|Lung(427;0.213)														---	---	---	---
PRKCZ	5590	broad.mit.edu	37	1	2110117	2110117	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2110117delC	uc001aiq.2	+						PRKCZ_uc001air.2_Intron|PRKCZ_uc010nyw.1_Intron|PRKCZ_uc001ais.2_Intron|PRKCZ_uc009vla.2_Intron|PRKCZ_uc010nyx.1_Intron|PRKCZ_uc001ait.2_Intron|uc001aiu.1_5'Flank	NM_002744	NP_002735			protein kinase C, zeta isoform 1						anti-apoptosis|intracellular signal transduction|negative regulation of insulin receptor signaling pathway|negative regulation of peptidyl-tyrosine phosphorylation|negative regulation of protein complex assembly|peptidyl-serine phosphorylation|platelet activation	endosome	ATP binding|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(2)	6	all_cancers(77;0.000177)|all_epithelial(69;6.41e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.96e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.3e-23)|GBM - Glioblastoma multiforme(42;2.85e-08)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00294)|BRCA - Breast invasive adenocarcinoma(365;0.00493)|STAD - Stomach adenocarcinoma(132;0.00669)|KIRC - Kidney renal clear cell carcinoma(229;0.0411)|Lung(427;0.213)														---	---	---	---
SKI	6497	broad.mit.edu	37	1	2240044	2240044	+	3'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2240044delT	uc001aja.3	+	7						NM_003036	NP_003027			v-ski sarcoma viral oncogene homolog						anterior/posterior axis specification|BMP signaling pathway|bone morphogenesis|cell motility|cell proliferation|embryonic limb morphogenesis|face morphogenesis|lens morphogenesis in camera-type eye|myelination in peripheral nervous system|myotube differentiation|negative regulation of activin receptor signaling pathway|negative regulation of BMP signaling pathway|negative regulation of fibroblast proliferation|negative regulation of osteoblast differentiation|negative regulation of Schwann cell proliferation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|neural tube closure|nose morphogenesis|olfactory bulb development|palate development|positive regulation of DNA binding|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway|protein homotrimerization|regulation of apoptosis|retina development in camera-type eye|skeletal muscle fiber development|SMAD protein signal transduction|somatic stem cell maintenance|transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	cytoplasm|PML body|transcription factor complex|transcriptional repressor complex	histone deacetylase inhibitor activity|nucleotide binding|protein domain specific binding|protein kinase binding|repressing transcription factor binding|SMAD binding|transcription corepressor activity|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding			lung(1)|central_nervous_system(1)	2	all_cancers(77;0.000139)|all_epithelial(69;4.45e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)			Epithelial(90;2.14e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.72e-29)|GBM - Glioblastoma multiforme(42;2.45e-08)|Colorectal(212;5.33e-05)|COAD - Colon adenocarcinoma(227;0.000228)|Kidney(185;0.00268)|BRCA - Breast invasive adenocarcinoma(365;0.00471)|STAD - Stomach adenocarcinoma(132;0.0147)|KIRC - Kidney renal clear cell carcinoma(229;0.0385)|Lung(427;0.207)														---	---	---	---
PRDM16	63976	broad.mit.edu	37	1	3097935	3097936	+	Intron	DEL	CG	-	-	rs143924929	by1000genomes;by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3097935_3097936delCG	uc001akf.2	+						PRDM16_uc001akc.2_Intron|PRDM16_uc001akd.2_Intron|PRDM16_uc001ake.2_Intron|PRDM16_uc009vlh.2_Intron	NM_022114	NP_071397			PR domain containing 16 isoform 1						brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)				T	EVI1	MDS|AML								---	---	---	---
TP73	7161	broad.mit.edu	37	1	3649253	3649253	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3649253delC	uc001akp.2	+						TP73_uc001akq.2_Intron|TP73_uc001akr.2_Intron|TP73_uc009vlk.1_Intron|TP73_uc001aks.2_Intron|TP73_uc010nzk.1_Intron|TP73_uc010nzl.1_Intron	NM_005427	NP_005418			tumor protein p73 isoform a						cellular response to UV|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mismatch repair|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of JUN kinase activity|negative regulation of neuron apoptosis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|protein tetramerization|response to gamma radiation|response to X-ray	chromatin|cytosol|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|metal ion binding|p53 binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding|transcription repressor activity			ovary(1)|lung(1)	2	all_cancers(77;0.0395)|Ovarian(185;0.0634)|Lung NSC(156;0.188)|all_lung(157;0.198)	all_epithelial(116;7.42e-17)|all_lung(118;1.86e-06)|Lung NSC(185;0.000163)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.109)|Ovarian(437;0.127)		Epithelial(90;5.57e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.87e-22)|GBM - Glioblastoma multiforme(42;5.72e-16)|Colorectal(212;2.22e-05)|COAD - Colon adenocarcinoma(227;8.48e-05)|Kidney(185;0.000539)|BRCA - Breast invasive adenocarcinoma(365;0.000868)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.00751)|Lung(427;0.226)														---	---	---	---
DFFB	1677	broad.mit.edu	37	1	3800481	3800481	+	3'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3800481delT	uc001alc.2	+	7					DFFB_uc001ale.2_RNA|DFFB_uc009vlp.2_RNA|DFFB_uc001alb.2_RNA|DFFB_uc010nzn.1_3'UTR|DFFB_uc009vlq.2_RNA|DFFB_uc009vlr.2_3'UTR|DFFB_uc001ald.2_3'UTR	NM_004402	NP_004393			DNA fragmentation factor, 40 kD, beta						apoptotic chromosome condensation|DNA fragmentation involved in apoptotic nuclear change|intracellular signal transduction	cytosol|nucleoplasm	deoxyribonuclease activity|enzyme binding				0	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_cancers(23;2.05e-30)|all_epithelial(116;6.22e-21)|all_lung(118;2.65e-08)|Lung NSC(185;6.25e-06)|Breast(487;0.000659)|Renal(390;0.00121)|all_neural(13;0.0019)|Hepatocellular(190;0.00705)|Colorectal(325;0.0113)|all_hematologic(16;0.0194)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0548)|Medulloblastoma(700;0.211)		Epithelial(90;1.18e-39)|OV - Ovarian serous cystadenocarcinoma(86;7.28e-23)|GBM - Glioblastoma multiforme(42;2.95e-17)|Colorectal(212;1.23e-05)|COAD - Colon adenocarcinoma(227;5.94e-05)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00038)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.124)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	5350260	5350262	+	IGR	DEL	GAA	-	-	rs143890959		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5350260_5350262delGAA								AJAP1 (506410 upstream) : NPHP4 (572608 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	5652080	5652081	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5652080_5652081delAC	uc001alp.1	-											Homo sapiens cDNA FLJ43088 fis, clone BRTHA3025826.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	5735261	5735263	+	IGR	DEL	CTC	-	-	rs139390359	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5735261_5735263delCTC								AJAP1 (891411 upstream) : NPHP4 (187607 downstream)																																			---	---	---	---
NPHP4	261734	broad.mit.edu	37	1	6050508	6050508	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6050508delA	uc001alq.1	-						NPHP4_uc001als.1_Intron|NPHP4_uc009vlt.1_Intron|NPHP4_uc001alt.1_Intron|KCNAB2_uc009vlv.1_5'Flank	NM_015102	NP_055917			nephroretinin						actin cytoskeleton organization|cell-cell adhesion|signal transduction|visual behavior	cell-cell junction|centrosome|cilium|microtubule basal body	protein binding|structural molecule activity			pancreas(1)	1	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
CHD5	26038	broad.mit.edu	37	1	6210428	6210431	+	Intron	DEL	GGAT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6210428_6210431delGGAT	uc001amb.1	-							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)														---	---	---	---
ACOT7	11332	broad.mit.edu	37	1	6408396	6408397	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6408396_6408397delAC	uc001ams.2	-						ACOT7_uc010nzq.1_Intron|ACOT7_uc001amt.2_Intron|ACOT7_uc001amu.2_Intron|ACOT7_uc001amv.2_Intron|ACOT7_uc001amq.2_Intron|ACOT7_uc001amr.2_Intron	NM_181864	NP_863654			acyl-CoA thioesterase 7 isoform hBACHb							mitochondrion|nucleus	carboxylesterase activity|fatty-acyl-CoA binding|palmitoyl-CoA hydrolase activity				0	Ovarian(185;0.0634)|all_lung(157;0.175)	all_cancers(23;1.42e-38)|all_epithelial(116;3.96e-23)|all_lung(118;3.69e-08)|Lung NSC(185;8.52e-07)|all_hematologic(16;6.92e-06)|Colorectal(325;4.53e-05)|Acute lymphoblastic leukemia(12;5e-05)|all_neural(13;0.000164)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;9.16e-37)|GBM - Glioblastoma multiforme(13;5.89e-29)|OV - Ovarian serous cystadenocarcinoma(86;7.63e-19)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;2.06e-05)|Kidney(185;7.74e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00129)|BRCA - Breast invasive adenocarcinoma(365;0.00132)|STAD - Stomach adenocarcinoma(132;0.00195)|READ - Rectum adenocarcinoma(331;0.0481)												OREG0013036	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	6470891	6470891	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6470891delT								ACOT7 (17065 upstream) : HES2 (1609 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	6821278	6821279	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6821278_6821279insA								DNAJC11 (59312 upstream) : CAMTA1 (24105 downstream)																																			---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	7427092	7427092	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7427092delA	uc001aoi.2	+							NM_015215	NP_056030			calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	8340777	8340777	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8340777delA								ERRFI1 (254384 upstream) : SLC45A1 (43613 downstream)																																			---	---	---	---
SLC45A1	50651	broad.mit.edu	37	1	8385486	8385486	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8385486delA	uc001apb.2	+							NM_001080397	NP_001073866			DNB5						carbohydrate transport	integral to membrane	symporter activity			central_nervous_system(2)|pancreas(1)|skin(1)	4	Ovarian(185;0.0661)|all_lung(157;0.127)	all_epithelial(116;1.22e-15)|all_lung(118;0.000147)|Lung NSC(185;0.000251)|Renal(390;0.000469)|Colorectal(325;0.00578)|Breast(348;0.00686)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;3.95e-66)|GBM - Glioblastoma multiforme(8;5.93e-33)|Colorectal(212;2.86e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00199)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
RERE	473	broad.mit.edu	37	1	8616315	8616316	+	Intron	INS	-	A	A	rs111743369		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8616315_8616316insA	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	9526690	9526690	+	IGR	DEL	A	-	-	rs78845867		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9526690delA								SPSB1 (97102 upstream) : SLC25A33 (72838 downstream)																																			---	---	---	---
SLC25A33	84275	broad.mit.edu	37	1	9612283	9612283	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9612283delT	uc001apw.2	+						SLC25A33_uc001apx.2_Intron	NM_032315	NP_115691			mitochondrial carrier protein MGC4399						transport	integral to membrane|mitochondrial inner membrane					0	all_lung(157;0.246)	all_epithelial(116;1.16e-18)|all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Breast(348;0.00191)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.01e-08)|COAD - Colon adenocarcinoma(227;1.44e-05)|Kidney(185;0.000262)|KIRC - Kidney renal clear cell carcinoma(229;0.000957)|BRCA - Breast invasive adenocarcinoma(304;0.0019)|STAD - Stomach adenocarcinoma(132;0.00355)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
SLC25A33	84275	broad.mit.edu	37	1	9625576	9625576	+	Intron	DEL	A	-	-	rs76465253		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9625576delA	uc001apw.2	+						SLC25A33_uc001apx.2_Intron	NM_032315	NP_115691			mitochondrial carrier protein MGC4399						transport	integral to membrane|mitochondrial inner membrane					0	all_lung(157;0.246)	all_epithelial(116;1.16e-18)|all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Breast(348;0.00191)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.01e-08)|COAD - Colon adenocarcinoma(227;1.44e-05)|Kidney(185;0.000262)|KIRC - Kidney renal clear cell carcinoma(229;0.000957)|BRCA - Breast invasive adenocarcinoma(304;0.0019)|STAD - Stomach adenocarcinoma(132;0.00355)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
CLSTN1	22883	broad.mit.edu	37	1	9806775	9806775	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9806775delA	uc001aqh.2	-						CLSTN1_uc001aqi.2_Intron|CLSTN1_uc010oag.1_Intron	NM_001009566	NP_001009566			calsyntenin 1 isoform 1						homophilic cell adhesion	cell junction|cell projection|endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nucleus|postsynaptic membrane	calcium ion binding			skin(1)	1	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	9978579	9978579	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9978579delA								CTNNBIP1 (8263 upstream) : LZIC (11199 downstream)																																			---	---	---	---
NMNAT1	64802	broad.mit.edu	37	1	10041299	10041299	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10041299delT	uc001aqp.2	+							NM_022787	NP_073624			nicotinamide mononucleotide adenylyltransferase						water-soluble vitamin metabolic process	nucleoplasm	ATP binding|nicotinamide-nucleotide adenylyltransferase activity|nicotinate-nucleotide adenylyltransferase activity|protein binding				0		all_lung(284;0.000407)|Renal(390;0.000469)|Lung NSC(185;0.000577)|Colorectal(325;0.0062)|Breast(348;0.00686)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.31e-08)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(185;0.00028)|BRCA - Breast invasive adenocarcinoma(304;0.00032)|KIRC - Kidney renal clear cell carcinoma(229;0.00101)|STAD - Stomach adenocarcinoma(132;0.00908)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
KIF1B	23095	broad.mit.edu	37	1	10385045	10385045	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10385045delA	uc001aqx.3	+						KIF1B_uc001aqw.3_Intron|KIF1B_uc001aqy.2_Intron|KIF1B_uc001aqz.2_Intron|KIF1B_uc001ara.2_Intron|KIF1B_uc001arb.2_Intron	NM_015074	NP_055889			kinesin family member 1B isoform b						anterograde axon cargo transport|apoptosis|neuromuscular synaptic transmission|neuron-neuron synaptic transmission	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|mitochondrion	ATP binding|ATPase activity|kinesin binding|microtubule motor activity|protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
PEX14	5195	broad.mit.edu	37	1	10573133	10573133	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10573133delT	uc001arn.2	+						PEX14_uc001arm.1_Intron|PEX14_uc009vmu.1_Intron|PEX14_uc009vmv.2_Intron|PEX14_uc010oam.1_Intron|PEX14_uc010oan.1_Intron|PEX14_uc001arl.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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	10883930	10883930	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10883930delA								CASZ1 (27223 upstream) : C1orf127 (122603 downstream)																																			---	---	---	---
MTOR	2475	broad.mit.edu	37	1	11175117	11175117	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11175117delA	uc001asd.2	-						MTOR_uc001asc.2_Intron	NM_004958	NP_004949			FK506 binding protein 12-rapamycin associated						cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29																		---	---	---	---
NPPA	4878	broad.mit.edu	37	1	11906978	11906980	+	Intron	DEL	CTT	-	-	rs150223468	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11906978_11906980delCTT	uc001ati.2	-						CLCN6_uc010oav.1_Intron|CLCN6_uc010oaw.1_Intron|CLCN6_uc010oax.1_Intron|CLCN6_uc010oay.1_Intron|CLCN6_uc010oaz.1_Intron|CLCN6_uc010oba.1_Intron	NM_006172	NP_006163			natriuretic peptide precursor A preproprotein						cGMP biosynthetic process|receptor guanylyl cyclase signaling pathway|regulation of blood pressure|regulation of blood vessel size	extracellular region	hormone activity			ovary(1)|central_nervous_system(1)	2	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00149)|all_lung(284;0.00189)|Breast(348;0.00586)|Colorectal(325;0.0062)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0556)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.04e-06)|COAD - Colon adenocarcinoma(227;0.000245)|BRCA - Breast invasive adenocarcinoma(304;0.000295)|Kidney(185;0.000733)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
VPS13D	55187	broad.mit.edu	37	1	12510180	12510180	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12510180delA	uc001atv.2	+						VPS13D_uc001atw.2_Intron|VPS13D_uc001atx.2_Intron|VPS13D_uc009vnl.2_Intron|VPS13D_uc010obd.1_Intron	NM_015378	NP_056193			vacuolar protein sorting 13D isoform 1						protein localization					ovary(4)|pancreas(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	12747800	12747801	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12747800_12747801delAA								AADACL4 (20704 upstream) : AADACL3 (28317 downstream)																																			---	---	---	---
PRAMEF11	440560	broad.mit.edu	37	1	12890542	12890543	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12890542_12890543insA	uc001auk.2	-							NM_001146344	NP_001139816			PRAME family member 11												0																		---	---	---	---
LOC440563	440563	broad.mit.edu	37	1	13184079	13184080	+	5'Flank	INS	-	T	T	rs146762683	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13184079_13184080insT	uc010obg.1	-							NM_001136561	NP_001130033			heterogeneous nuclear ribonucleoprotein C-like							ribonucleoprotein complex	nucleic acid binding|nucleotide binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	13218513	13218513	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13218513delA								LOC440563 (34546 upstream) : PRAMEF3 (110320 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	13832963	13832963	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13832963delT	uc001avb.2	-											RecName: Full=Leucine-rich repeat-containing protein 38; Flags: Precursor;																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	14276703	14276703	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14276703delC								PRDM2 (125131 upstream) : KAZ (648510 downstream)																																			---	---	---	---
KAZ	23254	broad.mit.edu	37	1	15216612	15216612	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15216612delG	uc001avm.3	+						KAZ_uc009vog.1_Intron|KAZ_uc010obj.1_Intron	NM_201628	NP_963922			kazrin isoform E						keratinization	cornified envelope|cytoplasm|desmosome|nucleus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	15558054	15558054	+	IGR	DEL	A	-	-	rs112496559		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15558054delA								TMEM51 (11081 upstream) : FHAD1 (15714 downstream)																																			---	---	---	---
EFHD2	79180	broad.mit.edu	37	1	15743312	15743312	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15743312delT	uc001awh.2	+							NM_024329	NP_077305			EF-hand domain family, member D2							membrane raft					0		Renal(390;0.00145)|Breast(348;0.00173)|Colorectal(325;0.00215)|all_lung(284;0.00366)|Lung NSC(340;0.00395)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)|Hepatocellular(190;0.152)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.59e-07)|COAD - Colon adenocarcinoma(227;3.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000119)|KIRC - Kidney renal clear cell carcinoma(229;0.00251)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
SPEN	23013	broad.mit.edu	37	1	16234923	16234923	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16234923delT	uc001axk.1	+						SPEN_uc010obp.1_Intron	NM_015001	NP_055816			spen homolog, transcriptional regulator						interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding			ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)														---	---	---	---
ZBTB17	7709	broad.mit.edu	37	1	16277579	16277579	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16277579delT	uc001axl.3	-						ZBTB17_uc010obq.1_Intron|ZBTB17_uc010obr.1_Intron|ZBTB17_uc010obs.1_Intron|ZBTB17_uc010obt.1_Intron|ZBTB17_uc010obu.1_Intron|ZBTB17_uc009vom.1_Intron|ZBTB17_uc010obv.1_Intron|ZBTB17_uc009von.1_Intron	NM_003443	NP_003434			zinc finger and BTB domain containing 17						negative regulation of cell cycle	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Colorectal(325;0.000257)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|Colorectal(212;4.12e-07)|COAD - Colon adenocarcinoma(227;2.43e-05)|BRCA - Breast invasive adenocarcinoma(304;9.97e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
FAM131C	348487	broad.mit.edu	37	1	16400993	16400994	+	5'Flank	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16400993_16400994delAC	uc001axz.3	-						FAM131C_uc010obz.1_5'Flank	NM_182623	NP_872429			hypothetical protein LOC348487												0		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	16517923	16517926	+	IGR	DEL	GGAG	-	-	rs111976774		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16517923_16517926delGGAG								EPHA2 (35359 upstream) : ARHGEF19 (6673 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	16980415	16980416	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16980415_16980416insA								MST1P2 (3501 upstream) : ESPNP (37297 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	17007961	17007962	+	IGR	INS	-	C	C	rs56359017		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17007961_17007962insC								MST1P2 (31047 upstream) : ESPNP (9751 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	17342368	17342369	+	IGR	INS	-	T	T	rs144538714	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17342368_17342369insT								ATP13A2 (3945 upstream) : SDHB (2858 downstream)																																			---	---	---	---
SDHB	6390	broad.mit.edu	37	1	17371412	17371412	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17371412delA	uc001bae.2	-							NM_003000	NP_002991			succinate dehydrogenase complex, subunit B, iron						respiratory electron transport chain|transport|tricarboxylic acid cycle	mitochondrial respiratory chain complex II	2 iron, 2 sulfur cluster binding|3 iron, 4 sulfur cluster binding|4 iron, 4 sulfur cluster binding|electron carrier activity|metal ion binding|protein binding|succinate dehydrogenase (ubiquinone) activity|ubiquinone binding			breast(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0049)|COAD - Colon adenocarcinoma(227;1.18e-05)|BRCA - Breast invasive adenocarcinoma(304;2.41e-05)|Kidney(64;0.000188)|KIRC - Kidney renal clear cell carcinoma(64;0.00273)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.19)	Succinic acid(DB00139)			Mis|N|F			paraganglioma|pheochromocytoma			Familial_Paragangliomas|Carney-Stratakis_syndrome|Cowden_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	1	17835041	17835042	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17835041_17835042insT								RCC2 (68821 upstream) : ARHGEF10L (31288 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	17846339	17846339	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17846339delA								RCC2 (80119 upstream) : ARHGEF10L (19991 downstream)																																			---	---	---	---
ARHGEF10L	55160	broad.mit.edu	37	1	17976382	17976382	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17976382delG	uc001ban.2	+						ARHGEF10L_uc009vpe.1_Intron|ARHGEF10L_uc001bao.2_Intron|ARHGEF10L_uc001bap.2_Intron|ARHGEF10L_uc001baq.2_Intron|ARHGEF10L_uc010ocs.1_Intron|ARHGEF10L_uc001bar.2_Intron|ARHGEF10L_uc009vpf.2_Intron	NM_018125	NP_060595			Rho guanine nucleotide exchange factor (GEF)						regulation of Rho protein signal transduction	cytoplasm	Rho guanyl-nucleotide exchange factor activity			large_intestine(1)|ovary(1)|pancreas(1)	3		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)														---	---	---	---
IGSF21	84966	broad.mit.edu	37	1	18445413	18445416	+	Intron	DEL	CCTT	-	-	rs72069989		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18445413_18445416delCCTT	uc001bau.1	+							NM_032880	NP_116269			immunoglobin superfamily, member 21 precursor							extracellular region				ovary(2)|large_intestine(1)|skin(1)	4		Colorectal(325;0.000147)|Renal(390;0.00145)|all_lung(284;0.00366)|Lung NSC(340;0.00376)|Breast(348;0.00387)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0121)|BRCA - Breast invasive adenocarcinoma(304;5.52e-05)|Kidney(64;0.00103)|KIRC - Kidney renal clear cell carcinoma(64;0.0102)|STAD - Stomach adenocarcinoma(196;0.0118)|READ - Rectum adenocarcinoma(331;0.157)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	19147303	19147304	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19147303_19147304delTG								PAX7 (71944 upstream) : TAS1R2 (18789 downstream)																																	OREG0013163	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
UBR4	23352	broad.mit.edu	37	1	19418471	19418471	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19418471delA	uc001bbi.2	-						UBR4_uc010ocv.1_Intron|UBR4_uc009vph.2_Intron|UBR4_uc010ocw.1_Intron|UBR4_uc001bbg.2_Intron|UBR4_uc001bbh.2_Intron	NM_020765	NP_065816			retinoblastoma-associated factor 600						interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)|skin(2)	25		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)														---	---	---	---
UBR4	23352	broad.mit.edu	37	1	19474752	19474753	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19474752_19474753delAA	uc001bbi.2	-						UBR4_uc001bbk.1_Intron	NM_020765	NP_065816			retinoblastoma-associated factor 600						interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)|skin(2)	25		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)														---	---	---	---
UBR4	23352	broad.mit.edu	37	1	19481287	19481287	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19481287delA	uc001bbi.2	-						UBR4_uc001bbk.1_5'Flank|UBR4_uc001bbl.1_Intron|UBR4_uc001bbm.1_Intron	NM_020765	NP_065816			retinoblastoma-associated factor 600						interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)|skin(2)	25		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)														---	---	---	---
MRTO4	51154	broad.mit.edu	37	1	19579313	19579313	+	Intron	DEL	T	-	-	rs112973544		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19579313delT	uc001bbs.2	+						KIAA0090_uc001bbo.2_5'Flank|KIAA0090_uc001bbp.2_5'Flank|KIAA0090_uc001bbq.2_5'Flank|KIAA0090_uc001bbr.2_5'Flank	NM_016183	NP_057267			mRNA turnover 4 homolog						ribosome biogenesis	nuclear membrane|nucleolus					0		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.87e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00301)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	19862156	19862156	+	IGR	DEL	A	-	-	rs112832971		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19862156delA								CAPZB (50164 upstream) : C1orf151 (61311 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	20164745	20164745	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20164745delA								RNF186 (22974 upstream) : OTUD3 (44143 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	20199766	20199767	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20199766_20199767insA								RNF186 (57995 upstream) : OTUD3 (9121 downstream)																																			---	---	---	---
VWA5B1	127731	broad.mit.edu	37	1	20673938	20673938	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20673938delT	uc009vps.2	+						VWA5B1_uc010odc.1_Intron|VWA5B1_uc001bde.3_Intron|VWA5B1_uc009vpt.2_Intron	NM_001039500	NP_001034589			von Willebrand factor A domain containing 5B1							extracellular region					0																		---	---	---	---
PINK1	65018	broad.mit.edu	37	1	20958557	20958558	+	5'Flank	DEL	CA	-	-	rs36116982		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20958557_20958558delCA	uc001bdm.2	+							NM_032409	NP_115785			PTEN induced putative kinase 1 precursor						cell death|intracellular protein kinase cascade|mitochondrion degradation|peptidyl-serine phosphorylation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of release of cytochrome c from mitochondria|regulation of protein complex assembly|regulation of protein ubiquitination|response to stress	cytosol|integral to membrane|mitochondrial outer membrane	ATP binding|C3HC4-type RING finger domain binding|calcium-dependent protein kinase activity|magnesium ion binding|protein serine/threonine kinase activity|ubiquitin protein ligase binding			ovary(2)|central_nervous_system(1)	3		all_lung(284;2.72e-05)|Lung NSC(340;2.94e-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;0.0182)|COAD - Colon adenocarcinoma(152;1.21e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000146)|Kidney(64;0.000182)|GBM - Glioblastoma multiforme(114;0.000497)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)														---	---	---	---
EIF4G3	8672	broad.mit.edu	37	1	21162436	21162437	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21162436_21162437delAA	uc001bec.2	-						EIF4G3_uc010odi.1_Intron|EIF4G3_uc010odj.1_Intron|EIF4G3_uc009vpz.2_Intron|EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bef.2_Intron|EIF4G3_uc001bee.2_Intron	NM_003760	NP_003751			eukaryotic translation initiation factor 4						interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity			skin(1)	1		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	21543102	21543102	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21543102delT								EIF4G3 (39762 upstream) : ECE1 (638 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	21683786	21683786	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21683786delT								ECE1 (11752 upstream) : NBPF3 (82845 downstream)																																			---	---	---	---
RAP1GAP	5909	broad.mit.edu	37	1	21931337	21931340	+	Intron	DEL	GATG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21931337_21931340delGATG	uc001bex.2	-						RAP1GAP_uc001bev.2_Intron|RAP1GAP_uc001bew.2_Intron|RAP1GAP_uc001bey.2_Intron	NM_002885	NP_002876			RAP1 GTPase activating protein isoform c						regulation of Ras GTPase activity|signal transduction	cytosol|Golgi membrane|membrane fraction	GTPase activator activity|GTPase activity|protein homodimerization activity|Ras GTPase binding			breast(2)|ovary(1)	3		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)														---	---	---	---
HSPG2	3339	broad.mit.edu	37	1	22249899	22249899	+	Intron	DEL	A	-	-	rs138565283		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22249899delA	uc001bfj.2	-						HSPG2_uc009vqd.2_Intron	NM_005529	NP_005520			heparan sulfate proteoglycan 2 precursor						angiogenesis|cell adhesion|lipid metabolic process|lipoprotein metabolic process	basement membrane|extracellular space|plasma membrane	protein C-terminus binding			ovary(5)|large_intestine(2)|central_nervous_system(1)|skin(1)	9		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Becaplermin(DB00102)|Palifermin(DB00039)													---	---	---	---
C1QB	713	broad.mit.edu	37	1	22978245	22978246	+	5'Flank	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22978245_22978246delAG	uc001bgd.2	+							NM_000491	NP_000482			complement component 1, q subcomponent, B chain						complement activation, classical pathway|innate immune response	collagen|complement component C1 complex				breast(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.06e-27)|Colorectal(126;1.58e-07)|GBM - Glioblastoma multiforme(114;6.72e-06)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000551)|KIRC - Kidney renal clear cell carcinoma(1967;0.0027)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)	Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)													---	---	---	---
LUZP1	7798	broad.mit.edu	37	1	23451432	23451432	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23451432delA	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	23571841	23571841	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23571841delA								HTR1D (50619 upstream) : HNRNPR (64436 downstream)																																			---	---	---	---
ASAP3	55616	broad.mit.edu	37	1	23779454	23779454	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23779454delG	uc001bha.2	-						ASAP3_uc010odz.1_Intron|ASAP3_uc010oea.1_Intron|ASAP3_uc001bhc.1_Intron	NM_017707	NP_060177			ArfGAP with SH3 domain, ankyrin repeat and PH						regulation of ARF GTPase activity	cytoplasm	ARF GTPase activator activity|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	23863946	23863947	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23863946_23863947insA								E2F2 (6233 upstream) : ID3 (20463 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	25454158	25454158	+	IGR	DEL	G	-	-	rs71674457		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25454158delG								RUNX3 (162546 upstream) : SYF2 (94609 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	25506263	25506263	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25506263delA								RUNX3 (214651 upstream) : SYF2 (42504 downstream)																																			---	---	---	---
TMEM57	55219	broad.mit.edu	37	1	25767687	25767687	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25767687delT	uc001bkk.2	+						TMEM57_uc009vru.2_Intron|TMEM57_uc009vrv.2_Intron|TMEM57_uc009vrt.2_Intron	NM_018202	NP_060672			transmembrane protein 57							axon|integral to membrane|neuron projection terminus|nuclear membrane|synapse part					0		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.00715)|all_lung(284;0.00989)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0675)|all_neural(195;0.201)		UCEC - Uterine corpus endometrioid carcinoma (279;0.042)|OV - Ovarian serous cystadenocarcinoma(117;1.85e-26)|Colorectal(126;2.99e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|STAD - Stomach adenocarcinoma(196;0.000766)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|GBM - Glioblastoma multiforme(114;0.0191)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	25855914	25855914	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25855914delT								TMEM57 (29218 upstream) : LDLRAP1 (14162 downstream)																																			---	---	---	---
SEPN1	57190	broad.mit.edu	37	1	26141993	26141993	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26141993delG	uc010oer.1	+						SEPN1_uc010oes.1_Intron	NM_020451	NP_065184			selenoprotein N, 1 isoform 1 precursor							endoplasmic reticulum membrane|extracellular region	protein binding			ovary(2)	2		Colorectal(325;3.46e-05)|Lung NSC(340;0.00038)|all_lung(284;0.00051)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0505)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0421)|OV - Ovarian serous cystadenocarcinoma(117;1.26e-25)|Colorectal(126;3.01e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|BRCA - Breast invasive adenocarcinoma(304;0.00099)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0143)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	26203316	26203317	+	IGR	INS	-	A	A	rs149961978	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26203316_26203317insA								PAQR7 (5572 upstream) : STMN1 (7361 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	26340444	26340444	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26340444delT								PAFAH2 (15796 upstream) : EXTL1 (7827 downstream)																																			---	---	---	---
UBXN11	91544	broad.mit.edu	37	1	26641580	26641580	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26641580delA	uc001bma.2	-						CD52_uc009vsg.1_5'Flank|CD52_uc001bmc.2_5'Flank	NM_145345	NP_663320			socius isoform 1							cytoplasm|cytoskeleton				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	26815937	26815938	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26815937_26815938delTT								HMGN2 (12806 upstream) : RPS6KA1 (40311 downstream)																																			---	---	---	---
RPS6KA1	6195	broad.mit.edu	37	1	26871667	26871669	+	Intron	DEL	TTC	-	-	rs4970486		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26871667_26871669delTTC	uc001bmr.1	+						RPS6KA1_uc010ofe.1_Intron|RPS6KA1_uc010off.1_Intron|RPS6KA1_uc001bms.1_5'Flank|RPS6KA1_uc009vsl.1_5'Flank	NM_002953	NP_002944			ribosomal protein S6 kinase, 90kDa, polypeptide						axon guidance|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|caspase inhibitor activity|magnesium ion binding|protein binding|protein serine/threonine kinase activity			lung(1)	1		all_cancers(24;2.49e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00571)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.12e-50)|OV - Ovarian serous cystadenocarcinoma(117;2.89e-29)|Colorectal(126;1.4e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000537)|KIRC - Kidney renal clear cell carcinoma(1967;0.000759)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0361)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.161)|LUSC - Lung squamous cell carcinoma(448;0.234)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	26992583	26992583	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26992583delT								RPS6KA1 (91063 upstream) : ARID1A (29939 downstream)																																			---	---	---	---
WASF2	10163	broad.mit.edu	37	1	27748318	27748318	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27748318delA	uc001bof.1	-						WASF2_uc010ofl.1_Intron	NM_006990	NP_008921			WAS protein family, member 2						actin cytoskeleton organization|G-protein signaling, coupled to cAMP nucleotide second messenger	actin cytoskeleton|lamellipodium	actin binding			skin(2)|ovary(1)	3		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0446)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.7e-08)|COAD - Colon adenocarcinoma(152;2e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00139)|KIRC - Kidney renal clear cell carcinoma(1967;0.00204)|STAD - Stomach adenocarcinoma(196;0.00325)|READ - Rectum adenocarcinoma(331;0.0481)														---	---	---	---
AHDC1	27245	broad.mit.edu	37	1	27880277	27880277	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27880277delA	uc009vsy.2	-						AHDC1_uc009vsz.1_Intron|AHDC1_uc001boh.1_Intron	NM_001029882	NP_001025053			AT hook, DNA binding motif, containing 1								DNA binding			central_nervous_system(1)	1		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)														---	---	---	---
RPA2	6118	broad.mit.edu	37	1	28223794	28223794	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28223794delA	uc001bpe.1	-						RPA2_uc001bpd.1_Intron|RPA2_uc010ofp.1_Intron	NM_002946	NP_002937			replication protein A2, 32kDa						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|regulation of double-strand break repair via homologous recombination|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor A complex|PML body	protein phosphatase binding|single-stranded DNA binding			skin(1)	1		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00588)|all_lung(284;0.00645)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0557)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0429)|OV - Ovarian serous cystadenocarcinoma(117;3.62e-24)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;1.75e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00294)|STAD - Stomach adenocarcinoma(196;0.00308)|BRCA - Breast invasive adenocarcinoma(304;0.00613)|READ - Rectum adenocarcinoma(331;0.0649)									Direct_reversal_of_damage|NER					---	---	---	---
EYA3	2140	broad.mit.edu	37	1	28304728	28304728	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28304728delA	uc001bpi.1	-						EYA3_uc010ofs.1_Intron|EYA3_uc010oft.1_Intron|EYA3_uc001bpj.2_Intron	NM_001990	NP_001981			eyes absent 3						anatomical structure morphogenesis|double-strand break repair|histone dephosphorylation|multicellular organismal development|positive regulation of DNA repair|regulation of transcription, DNA-dependent|response to ionizing radiation|transcription, DNA-dependent|visual perception	cytoplasm	metal ion binding|protein binding|protein tyrosine phosphatase activity			ovary(2)|skin(1)	3		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000432)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0484)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;2.8e-06)|STAD - Stomach adenocarcinoma(196;0.00364)|KIRC - Kidney renal clear cell carcinoma(1967;0.00378)|BRCA - Breast invasive adenocarcinoma(304;0.00718)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
PTAFR	5724	broad.mit.edu	37	1	28492296	28492296	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28492296delA	uc001bpl.2	-						PTAFR_uc001bpm.3_Intron|PTAFR_uc009vte.2_Intron	NM_000952	NP_000943			platelet-activating factor receptor						chemotaxis|inflammatory response|interferon-gamma-mediated signaling pathway|phosphatidylinositol-mediated signaling	integral to plasma membrane|nucleus	phospholipid binding|platelet activating factor receptor activity				0		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00715)|all_lung(284;0.00732)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0557)		UCEC - Uterine corpus endometrioid carcinoma (279;0.215)|OV - Ovarian serous cystadenocarcinoma(117;6e-22)|Colorectal(126;3.04e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00279)|BRCA - Breast invasive adenocarcinoma(304;0.00595)|STAD - Stomach adenocarcinoma(196;0.00678)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
SESN2	83667	broad.mit.edu	37	1	28602263	28602263	+	Intron	DEL	A	-	-	rs78168823		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28602263delA	uc001bps.2	+							NM_031459	NP_113647			sestrin 2						cell cycle arrest	cytoplasm|nucleus				skin(3)|ovary(2)|pancreas(1)|lung(1)	7		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;4.76e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;2.98e-22)|Colorectal(126;3.04e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00279)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00595)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PHACTR4	65979	broad.mit.edu	37	1	28817970	28817970	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28817970delA	uc001bpw.2	+						PHACTR4_uc001bpv.1_Intron|PHACTR4_uc001bpx.2_Intron|PHACTR4_uc001bpy.2_Intron|PHACTR4_uc001bpz.2_5'Flank	NM_001048183	NP_001041648			phosphatase and actin regulator 4 isoform 1								actin binding|protein phosphatase inhibitor activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	28929298	28929299	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28929298_28929299insA								RAB42 (8212 upstream) : TAF12 (312 downstream)																																			---	---	---	---
TAF12	6883	broad.mit.edu	37	1	28946461	28946461	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28946461delA	uc001bqw.2	-						TAF12_uc001bqx.2_Intron|TAF12_uc001bqy.2_Intron|TAF12_uc009vti.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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	29045462	29045462	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29045462delT								GMEB1 (4077 upstream) : YTHDF2 (17674 downstream)																																			---	---	---	---
EPB41	2035	broad.mit.edu	37	1	29338635	29338636	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29338635_29338636delTT	uc001brm.1	+						EPB41_uc001brg.1_Intron|EPB41_uc001brh.1_Intron|EPB41_uc001bri.1_Intron|EPB41_uc001brj.1_Intron|EPB41_uc009vtk.1_Intron|EPB41_uc001brk.2_Intron|EPB41_uc001brl.1_Intron|EPB41_uc009vtl.1_Intron|EPB41_uc009vtm.1_Intron	NM_203342	NP_976217			erythrocyte membrane protein band 4.1						blood circulation|cortical actin cytoskeleton organization|positive regulation of protein binding	extrinsic to membrane|Golgi apparatus|nucleus|plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	1-phosphatidylinositol binding|actin binding|spectrin binding|structural constituent of cytoskeleton			ovary(1)	1		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	29513154	29513154	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29513154delT								SFRS4 (4517 upstream) : MECR (6231 downstream)																																			---	---	---	---
MECR	51102	broad.mit.edu	37	1	29526132	29526132	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29526132delT	uc001brq.1	-						MECR_uc001brp.1_Intron|MECR_uc001brr.1_Intron|MECR_uc001brs.1_Intron	NM_016011	NP_057095			trans-2-enoyl-CoA reductase, mitochondrial						fatty acid biosynthetic process	mitochondrion	trans-2-enoyl-CoA reductase (NADPH) activity|zinc ion binding			ovary(1)	1		Colorectal(325;0.000389)|Breast(348;0.00765)|Lung NSC(340;0.0081)|all_lung(284;0.00914)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.39e-07)|COAD - Colon adenocarcinoma(152;2.04e-05)|STAD - Stomach adenocarcinoma(196;0.0195)|BRCA - Breast invasive adenocarcinoma(304;0.053)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.137)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	30048791	30048791	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30048791delA								PTPRU (395476 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	30129060	30129061	+	IGR	INS	-	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30129060_30129061insC								PTPRU (475745 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	31235790	31235792	+	IGR	DEL	AAG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31235790_31235792delAAG								LAPTM5 (5107 upstream) : SDC3 (106521 downstream)																																			---	---	---	---
PUM1	9698	broad.mit.edu	37	1	31459400	31459401	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31459400_31459401delAA	uc001bsi.1	-						PUM1_uc001bsf.1_Intron|PUM1_uc001bsg.1_Intron|PUM1_uc001bsh.1_Intron|PUM1_uc001bsj.1_Intron|PUM1_uc010oga.1_Intron|PUM1_uc001bsk.1_Intron|PUM1_uc010ogb.1_Intron|PRO0611_uc001bsm.2_5'Flank	NM_014676	NP_055491			pumilio 1 isoform 2						cellular membrane organization|post-Golgi vesicle-mediated transport|regulation of translation	cytosol	RNA binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)														---	---	---	---
NKAIN1	79570	broad.mit.edu	37	1	31665403	31665404	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31665403_31665404delTT	uc010ogd.1	-							NM_024522	NP_078798			Na+/K+ transporting ATPase interacting 1							integral to membrane|plasma membrane				ovary(1)	1		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)|Breast(348;0.141)|all_neural(195;0.146)|Medulloblastoma(700;0.151)		STAD - Stomach adenocarcinoma(196;0.0184)|READ - Rectum adenocarcinoma(331;0.148)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	32332958	32332958	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32332958delC								SPOCD1 (51378 upstream) : PTP4A2 (40835 downstream)																																			---	---	---	---
HDAC1	3065	broad.mit.edu	37	1	32776457	32776457	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32776457delA	uc001bvb.1	+						HDAC1_uc010ohd.1_Intron|HDAC1_uc010ohe.1_Intron|HDAC1_uc010ohf.1_Intron	NM_004964	NP_004955			histone deacetylase 1						anti-apoptosis|blood coagulation|embryonic digit morphogenesis|epidermal cell differentiation|eyelid development in camera-type eye|fungiform papilla formation|hair follicle placode formation|histone H3 deacetylation|histone H4 deacetylation|negative regulation by host of viral transcription|negative regulation of androgen receptor signaling pathway|negative regulation of cell cycle|nerve growth factor receptor signaling pathway|odontogenesis of dentine-containing tooth|positive regulation of cell proliferation|positive regulation of receptor biosynthetic process|positive regulation of transcription from RNA polymerase II promoter	cytosol|NuRD complex|Sin3 complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|identical protein binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|RNA polymerase II transcription corepressor activity|sequence-specific DNA binding transcription factor activity			ovary(1)|lung(1)|breast(1)	3		Breast(348;0.000523)|Lung NSC(340;0.000992)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Lung SC(1967;0.113)		KIRC - Kidney renal clear cell carcinoma(1967;0.138)	Vorinostat(DB02546)													---	---	---	---
BSDC1	55108	broad.mit.edu	37	1	32834302	32834302	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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)																---	---	---	---
ZBTB8OS	339487	broad.mit.edu	37	1	33100582	33100582	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33100582delT	uc001bvp.2	-						ZBTB8OS_uc001bvo.1_Intron|ZBTB8OS_uc001bvq.2_Intron	NM_178547	NP_848642			zinc finger and BTB domain containing 8 opposite												0		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)																---	---	---	---
S100PBP	64766	broad.mit.edu	37	1	33311285	33311287	+	Intron	DEL	TTT	-	-	rs11579954	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33311285_33311287delTTT	uc001bvz.2	+						S100PBP_uc001bwc.2_Intron|S100PBP_uc001bwd.2_Intron	NM_022753	NP_073590			S100P binding protein isoform a							nucleus	calcium-dependent protein binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	33446130	33446130	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33446130delA								RNF19B (15844 upstream) : AK2 (27456 downstream)																																			---	---	---	---
CSMD2	114784	broad.mit.edu	37	1	34094666	34094667	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34094666_34094667delAA	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	34175032	34175032	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34175032delA	uc001bxn.1	-						CSMD2_uc001bxm.1_Intron|CSMD2_uc001bxo.1_5'UTR	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	34526253	34526255	+	Intron	DEL	TTT	-	-	rs112747275		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34526253_34526255delTTT	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)																---	---	---	---
KIAA0319L	79932	broad.mit.edu	37	1	35933294	35933294	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35933294delT	uc001byx.2	-						KIAA0319L_uc010ohv.1_Intron|KIAA0319L_uc010ohw.1_Intron|KIAA0319L_uc001byz.2_Intron|KIAA0319L_uc010ohx.1_Intron	NM_024874	NP_079150			dyslexia susceptibility 2-like							cytoplasmic vesicle part|integral to membrane	protein binding			skin(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	36795306	36795306	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36795306delA								C1orf113 (4822 upstream) : STK40 (9919 downstream)																																			---	---	---	---
GRIK3	2899	broad.mit.edu	37	1	37498088	37498088	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37498088delG	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	38110151	38110152	+	IGR	INS	-	TG	TG	rs141886982	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38110151_38110152insTG								RSPO1 (9660 upstream) : C1orf109 (37098 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	38135427	38135430	+	IGR	DEL	CCTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38135427_38135430delCCTT								RSPO1 (34936 upstream) : C1orf109 (11820 downstream)																																			---	---	---	---
INPP5B	3633	broad.mit.edu	37	1	38392967	38392967	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38392967delA	uc001ccg.1	-						INPP5B_uc009vvk.1_Intron|INPP5B_uc001ccf.1_Intron	NM_005540	NP_005531			inositol polyphosphate-5-phosphatase, 75kDa						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|integral to membrane|microtubule cytoskeleton	GTPase activator activity|inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|protein binding			urinary_tract(1)	1	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)																---	---	---	---
SF3A3	10946	broad.mit.edu	37	1	38427764	38427764	+	Intron	DEL	C	-	-	rs112927427		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38427764delC	uc001cci.2	-						SF3A3_uc010oik.1_Intron	NM_006802	NP_006793			splicing factor 3a, subunit 3						nuclear mRNA 3'-splice site recognition	catalytic step 2 spliceosome|nuclear speck	nucleic acid binding|protein binding|zinc ion binding				0	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	38925033	38925033	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38925033delC								POU3F1 (412583 upstream) : RRAGC (379982 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	39025761	39025761	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39025761delA								POU3F1 (513311 upstream) : RRAGC (279254 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	39232244	39232245	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39232244_39232245delTT								POU3F1 (719794 upstream) : RRAGC (72770 downstream)																																			---	---	---	---
MACF1	23499	broad.mit.edu	37	1	39546049	39546052	+	5'Flank	DEL	TGAA	-	-	rs146071700		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39546049_39546052delTGAA	uc010ois.1	+						MACF1_uc010oir.1_5'Flank	NM_012090	NP_036222			microfilament and actin filament cross-linker						cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)															---	---	---	---
MACF1	23499	broad.mit.edu	37	1	39791622	39791623	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39791622_39791623insT	uc010ois.1	+						MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron|MACF1_uc001cdb.1_Intron	NM_012090	NP_036222			microfilament and actin filament cross-linker						cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)															---	---	---	---
MACF1	23499	broad.mit.edu	37	1	39898480	39898480	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39898480delT	uc010oiu.1	+						MACF1_uc010ois.1_Intron|MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron	NM_033044	NP_149033			microfilament and actin filament cross-linker						cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)															---	---	---	---
HPCAL4	51440	broad.mit.edu	37	1	40148562	40148562	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40148562delT	uc001cdr.2	-						HPCAL4_uc010oix.1_Intron	NM_016257	NP_057341			hippocalcin-like protein 4						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)															---	---	---	---
MFSD2A	84879	broad.mit.edu	37	1	40429116	40429116	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40429116delA	uc001cev.2	+						MFSD2A_uc010ojb.1_Intron|MFSD2A_uc001ceu.2_Intron|MFSD2A_uc010ojc.1_Intron|MFSD2A_uc009vvy.2_Intron	NM_001136493	NP_001129965			major facilitator superfamily domain containing						transmembrane transport	endoplasmic reticulum membrane|integral to membrane				ovary(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	40708125	40708126	+	IGR	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40708125_40708126delCT								RLF (1533 upstream) : TMCO2 (5447 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	41879485	41879488	+	IGR	DEL	ACAC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41879485_41879488delACAC								SCMH1 (171697 upstream) : EDN2 (64961 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	42612502	42612502	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42612502delC								HIVEP3 (110906 upstream) : GUCA2B (6590 downstream)																																	OREG0013419	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
RIMKLA	284716	broad.mit.edu	37	1	42855142	42855145	+	Intron	DEL	GAGA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42855142_42855145delGAGA	uc001chi.2	+							NM_173642	NP_775913			ribosomal modification protein rimK-like family						protein modification process	cytoplasm	acid-amino acid ligase activity|ATP binding|metal ion binding				0																		---	---	---	---
RIMKLA	284716	broad.mit.edu	37	1	42859302	42859304	+	Intron	DEL	AAT	-	-	rs5773772		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42859302_42859304delAAT	uc001chi.2	+							NM_173642	NP_775913			ribosomal modification protein rimK-like family						protein modification process	cytoplasm	acid-amino acid ligase activity|ATP binding|metal ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	43601023	43601023	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43601023delG	uc009vwn.1	+											Homo sapiens cDNA, FLJ99785.																														---	---	---	---
MPL	4352	broad.mit.edu	37	1	43808224	43808224	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43808224delA	uc001ciw.2	+						MPL_uc001civ.2_Intron|MPL_uc009vwr.2_Intron	NM_005373	NP_005364			myeloproliferative leukemia virus oncogene						cell proliferation|platelet activation	integral to plasma membrane	cytokine receptor activity			haematopoietic_and_lymphoid_tissue(361)|upper_aerodigestive_tract(1)|pancreas(1)	363	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)						Mis		MPD	MPD	congenital amegakaryocytic thrombocytopenia						---	---	---	---
ST3GAL3	6487	broad.mit.edu	37	1	44293011	44293011	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44293011delA	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)																---	---	---	---
ERI3	79033	broad.mit.edu	37	1	44696961	44696961	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44696961delT	uc001clt.2	-						ERI3_uc010okv.1_Intron|ERI3_uc009vxg.2_Intron|ERI3_uc010okw.1_Intron|ERI3_uc001clu.2_Intron	NM_024066	NP_076971			prion protein interacting protein							intracellular	exonuclease activity|metal ion binding|nucleic acid binding			ovary(2)|large_intestine(1)	3																		---	---	---	---
RNF220	55182	broad.mit.edu	37	1	44948300	44948300	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44948300delT	uc001clv.1	+						RNF220_uc001clw.1_Intron|RNF220_uc010okx.1_Intron|RNF220_uc010oky.1_Intron	NM_018150	NP_060620			ring finger protein 220						protein autoubiquitination	cytoplasm	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
EIF2B3	8891	broad.mit.edu	37	1	45392811	45392813	+	Intron	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45392811_45392813delAAA	uc001cmt.1	-						EIF2B3_uc001cmu.1_Intron|EIF2B3_uc001cmv.1_Intron|EIF2B3_uc001cmw.2_Intron	NM_020365	NP_065098			eukaryotic translation initiation factor 2B,						negative regulation of translational initiation in response to stress|oligodendrocyte development|response to glucose stimulus|response to heat|response to peptide hormone stimulus	cytosol|eukaryotic translation initiation factor 2B complex	nucleotidyltransferase activity|protein binding|translation initiation factor activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
TESK2	10420	broad.mit.edu	37	1	45821220	45821220	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45821220delT	uc001cns.1	-						TESK2_uc009vxr.1_Intron|TESK2_uc010olo.1_Intron|TESK2_uc009vxs.1_Intron	NM_007170	NP_009101			testis-specific protein kinase 2						actin cytoskeleton organization|focal adhesion assembly|spermatogenesis	nucleus	ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(2)|breast(2)|pancreas(1)	5	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
MAST2	23139	broad.mit.edu	37	1	46267182	46267182	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46267182delT	uc001cov.2	+						MAST2_uc001cow.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	46535191	46535191	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46535191delA	uc001cpb.3	-						PIK3R3_uc009vyb.2_Intron|PIK3R3_uc009vyc.2_Intron|PIK3R3_uc001cpc.3_Intron|PIK3R3_uc010olw.1_Intron	NM_003629	NP_003620			phosphoinositide-3-kinase, regulatory subunit 3						insulin receptor signaling pathway|platelet activation|T cell costimulation		1-phosphatidylinositol-3-kinase activity|protein binding				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
PIK3R3	8503	broad.mit.edu	37	1	46594746	46594748	+	Intron	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46594746_46594748delAAA	uc001cpb.3	-						PIK3R3_uc009vyb.2_Intron|PIK3R3_uc009vyc.2_Intron|PIK3R3_uc001cpc.3_Intron|PIK3R3_uc010olw.1_Intron	NM_003629	NP_003620			phosphoinositide-3-kinase, regulatory subunit 3						insulin receptor signaling pathway|platelet activation|T cell costimulation		1-phosphatidylinositol-3-kinase activity|protein binding				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
CYP4B1	1580	broad.mit.edu	37	1	47264499	47264499	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47264499delT	uc001cqm.3	+						CYP4B1_uc009vyl.1_5'Flank|CYP4B1_uc001cqn.3_5'Flank|CYP4B1_uc009vym.2_5'Flank|CYP4B1_uc010omk.1_5'Flank	NM_000779	NP_000770			cytochrome P450, family 4, subfamily B,						xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
STIL	6491	broad.mit.edu	37	1	47752002	47752002	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47752002delT	uc001crc.1	-						TAL1_uc001crb.1_Intron|STIL_uc010omn.1_Intron|STIL_uc010omo.1_Intron|STIL_uc001crd.1_Intron|STIL_uc001cre.1_Intron|STIL_uc001crf.1_5'Flank|STIL_uc001crg.1_Intron	NM_003035	NP_003026			SCL/TAL1 interrupting locus isoform 2						cell proliferation|multicellular organismal development	centrosome|cytosol				lung(2)|skin(1)	3		Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444)																---	---	---	---
AGBL4	84871	broad.mit.edu	37	1	50252735	50252735	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50252735delC	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron	NM_032785	NP_116174			ATP/GTP binding protein-like 4						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)														---	---	---	---
ELAVL4	1996	broad.mit.edu	37	1	50642690	50642691	+	Intron	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50642690_50642691delCT	uc001csb.2	+						ELAVL4_uc001cry.3_Intron|ELAVL4_uc001crz.3_Intron|ELAVL4_uc001csa.3_Intron|ELAVL4_uc001csc.3_Intron|ELAVL4_uc009vyu.2_Intron|ELAVL4_uc010omz.1_Intron	NM_021952	NP_068771			ELAV-like 4 isoform 1						mRNA processing		AU-rich element binding|mRNA 3'-UTR binding|nucleotide binding			ovary(1)|pancreas(1)	2																		---	---	---	---
FAF1	11124	broad.mit.edu	37	1	51061719	51061719	+	Intron	DEL	A	-	-	rs74080024	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51061719delA	uc009vyx.1	-						FAF1_uc009vyw.1_Intron|FAF1_uc001cse.1_Intron|FAF1_uc010onc.1_Intron	NM_007051	NP_008982			FAS-associated factor 1						apoptosis|cytoplasmic sequestering of NF-kappaB|positive regulation of apoptosis|positive regulation of protein complex assembly|proteasomal ubiquitin-dependent protein catabolic process|regulation of protein catabolic process	CD95 death-inducing signaling complex|cytosol|perinuclear region of cytoplasm	heat shock protein binding|NF-kappaB binding|protein kinase binding|protein kinase regulator activity			ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)														---	---	---	---
FAF1	11124	broad.mit.edu	37	1	51135232	51135232	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51135232delA	uc009vyx.1	-						FAF1_uc009vyw.1_Intron|FAF1_uc001cse.1_Intron	NM_007051	NP_008982			FAS-associated factor 1						apoptosis|cytoplasmic sequestering of NF-kappaB|positive regulation of apoptosis|positive regulation of protein complex assembly|proteasomal ubiquitin-dependent protein catabolic process|regulation of protein catabolic process	CD95 death-inducing signaling complex|cytosol|perinuclear region of cytoplasm	heat shock protein binding|NF-kappaB binding|protein kinase binding|protein kinase regulator activity			ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)														---	---	---	---
FAF1	11124	broad.mit.edu	37	1	51264562	51264562	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51264562delT	uc009vyx.1	-						FAF1_uc009vyw.1_Intron|FAF1_uc001cse.1_Intron	NM_007051	NP_008982			FAS-associated factor 1						apoptosis|cytoplasmic sequestering of NF-kappaB|positive regulation of apoptosis|positive regulation of protein complex assembly|proteasomal ubiquitin-dependent protein catabolic process|regulation of protein catabolic process	CD95 death-inducing signaling complex|cytosol|perinuclear region of cytoplasm	heat shock protein binding|NF-kappaB binding|protein kinase binding|protein kinase regulator activity			ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	51464586	51464587	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51464586_51464587insA								CDKN2C (24279 upstream) : C1orf185 (103319 downstream)														p.0?(2)|p.?(1)																					---	---	---	---
EPS15	2060	broad.mit.edu	37	1	51868089	51868089	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51868089delA	uc001csq.1	-						EPS15_uc009vyz.1_Intron|EPS15_uc001csp.3_Intron	NM_001981	NP_001972			epidermal growth factor receptor pathway						cell proliferation|clathrin coat assembly|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|protein transport	cytosol|early endosome membrane	calcium ion binding|SH3 domain binding			lung(1)|kidney(1)	2								T	MLL	ALL								---	---	---	---
EPS15	2060	broad.mit.edu	37	1	51922981	51922981	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51922981delA	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								---	---	---	---
EPS15	2060	broad.mit.edu	37	1	51978678	51978678	+	Intron	DEL	T	-	-	rs72674571	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51978678delT	uc001csq.1	-						EPS15_uc009vyz.1_Intron|EPS15_uc001csr.1_Intron	NM_001981	NP_001972			epidermal growth factor receptor pathway						cell proliferation|clathrin coat assembly|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|protein transport	cytosol|early endosome membrane	calcium ion binding|SH3 domain binding			lung(1)|kidney(1)	2								T	MLL	ALL								---	---	---	---
ZFYVE9	9372	broad.mit.edu	37	1	52810259	52810259	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52810259delT	uc001cto.2	+						ZFYVE9_uc001ctp.2_Intron	NM_004799	NP_004790			zinc finger, FYVE domain containing 9 isoform 3						endocytosis|SMAD protein complex assembly|SMAD protein import into nucleus|transforming growth factor beta receptor signaling pathway	early endosome membrane	metal ion binding|protein binding|receptor activity|serine-type peptidase activity			ovary(2)|lung(2)|central_nervous_system(2)|skin(2)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	53027472	53027473	+	IGR	DEL	AA	-	-	rs72141042		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53027472_53027473delAA								ZCCHC11 (8342 upstream) : GPX7 (40570 downstream)																																			---	---	---	---
C1orf163	65260	broad.mit.edu	37	1	53153917	53153918	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53153917_53153918delTT	uc001cui.1	-							NM_023077	NP_075565			hypothetical protein LOC65260								binding				0																		---	---	---	---
PODN	127435	broad.mit.edu	37	1	53531028	53531028	+	Intron	DEL	A	-	-	rs72270227		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53531028delA	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																		---	---	---	---
LRP8	7804	broad.mit.edu	37	1	53796178	53796185	+	5'Flank	DEL	AAGGAAGG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53796178_53796185delAAGGAAGG	uc001cvk.1	-						LRP8_uc001cvi.1_5'Flank|LRP8_uc001cvj.1_5'Flank|LRP8_uc001cvl.1_5'Flank|uc001cvn.1_Intron	NM_033300	NP_150643			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																		---	---	---	---
CYB5RL	606495	broad.mit.edu	37	1	54658434	54658434	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54658434delT	uc009vzo.2	-						CYB5RL_uc001cww.2_Intron|CYB5RL_uc001cwx.3_Intron|CYB5RL_uc001cwy.3_Intron	NM_001031672	NP_001026842			cytochrome b5 reductase-like								cytochrome-b5 reductase activity				0																		---	---	---	---
SSBP3	23648	broad.mit.edu	37	1	54774441	54774441	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54774441delA	uc001cxe.2	-						SSBP3_uc001cxf.2_Intron|SSBP3_uc001cxg.2_Intron	NM_145716	NP_663768			single stranded DNA binding protein 3 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	single-stranded DNA binding				0																		---	---	---	---
SSBP3	23648	broad.mit.edu	37	1	54816517	54816517	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54816517delT	uc001cxe.2	-						SSBP3_uc001cxf.2_Intron|SSBP3_uc001cxg.2_Intron	NM_145716	NP_663768			single stranded DNA binding protein 3 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	single-stranded DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	54877152	54877152	+	IGR	DEL	A	-	-	rs113234265		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54877152delA								SSBP3 (5060 upstream) : ACOT11 (130778 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	54878397	54878397	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54878397delT								SSBP3 (6305 upstream) : ACOT11 (129533 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	54980407	54980407	+	IGR	DEL	A	-	-	rs59885411	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54980407delA								SSBP3 (108315 upstream) : ACOT11 (27523 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	56214315	56214315	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56214315delT								USP24 (533553 upstream) : PPAP2B (746118 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	56221537	56221537	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56221537delT								USP24 (540775 upstream) : PPAP2B (738896 downstream)																																			---	---	---	---
PPAP2B	8613	broad.mit.edu	37	1	57046556	57046556	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57046556delT	uc001cyj.1	-							NM_177414	NP_803133			phosphatidic acid phosphatase type 2B						canonical Wnt receptor signaling pathway involved in positive regulation of cell-cell adhesion|canonical Wnt receptor signaling pathway involved in positive regulation of endothelial cell migration|canonical Wnt receptor signaling pathway involved in positive regulation of wound healing|germ cell migration|homotypic cell-cell adhesion|negative regulation of protein phosphorylation|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|sphingolipid metabolic process	adherens junction|Golgi apparatus|integral to membrane	phosphatidate phosphatase activity|phosphoprotein phosphatase activity|protein binding|sphingosine-1-phosphate phosphatase activity				0																		---	---	---	---
C8B	732	broad.mit.edu	37	1	57424169	57424169	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57424169delA	uc001cyp.2	-						C8B_uc010oon.1_Intron|C8B_uc010ooo.1_Intron	NM_000066	NP_000057			complement component 8, beta polypeptide						complement activation, alternative pathway|complement activation, classical pathway|cytolysis	membrane attack complex				central_nervous_system(2)|large_intestine(1)|ovary(1)	4																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	57867741	57867741	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57867741delA	uc001cys.1	-						DAB1_uc001cyt.1_Intron|DAB1_uc009vzx.1_Intron	NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	59008248	59008248	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59008248delA	uc001cyt.1	-						OMA1_uc001cyy.2_Intron|OMA1_uc009vzz.2_Intron	NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	59559920	59559920	+	IGR	DEL	A	-	-	rs149939792	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59559920delA								JUN (310135 upstream) : LOC729467 (37690 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	59591443	59591443	+	IGR	DEL	T	-	-	rs113455226		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59591443delT								JUN (341658 upstream) : LOC729467 (6167 downstream)																																			---	---	---	---
FGGY	55277	broad.mit.edu	37	1	59933170	59933170	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59933170delA	uc001czi.3	+						FGGY_uc001czg.2_Intron|FGGY_uc001czh.2_Intron|FGGY_uc009wac.2_Intron|FGGY_uc001czj.3_Intron|FGGY_uc001czk.3_Intron|FGGY_uc001czl.3_Intron	NM_018291	NP_060761			FGGY carbohydrate kinase domain containing						carbohydrate metabolic process|cell death|neuron homeostasis		kinase activity|phosphotransferase activity, alcohol group as acceptor			ovary(1)	1	all_cancers(7;7.36e-05)																	---	---	---	---
FGGY	55277	broad.mit.edu	37	1	60223475	60223475	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60223475delA	uc001czi.3	+						FGGY_uc009wac.2_Intron|FGGY_uc001czj.3_Intron|FGGY_uc001czk.3_Intron|FGGY_uc001czl.3_Intron|FGGY_uc001czm.3_Intron	NM_018291	NP_060761			FGGY carbohydrate kinase domain containing						carbohydrate metabolic process|cell death|neuron homeostasis		kinase activity|phosphotransferase activity, alcohol group as acceptor			ovary(1)	1	all_cancers(7;7.36e-05)																	---	---	---	---
FGGY	55277	broad.mit.edu	37	1	60223711	60223712	+	Intron	INS	-	AC	AC			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60223711_60223712insAC	uc001czi.3	+						FGGY_uc009wac.2_Intron|FGGY_uc001czj.3_Intron|FGGY_uc001czk.3_Intron|FGGY_uc001czl.3_Intron|FGGY_uc001czm.3_Intron	NM_018291	NP_060761			FGGY carbohydrate kinase domain containing						carbohydrate metabolic process|cell death|neuron homeostasis		kinase activity|phosphotransferase activity, alcohol group as acceptor			ovary(1)	1	all_cancers(7;7.36e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	61324557	61324557	+	IGR	DEL	T	-	-	rs68188974		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61324557delT								C1orf87 (785131 upstream) : NFIA (218389 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	61453712	61453713	+	IGR	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61453712_61453713delCT								C1orf87 (914286 upstream) : NFIA (89233 downstream)																																			---	---	---	---
INADL	10207	broad.mit.edu	37	1	62231063	62231064	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62231063_62231064delTT	uc001dab.2	+						INADL_uc009waf.1_Intron|INADL_uc001daa.2_Intron	NM_176877	NP_795352			InaD-like						intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4																		---	---	---	---
INADL	10207	broad.mit.edu	37	1	62396380	62396380	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62396380delT	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																		---	---	---	---
INADL	10207	broad.mit.edu	37	1	62618328	62618328	+	Intron	DEL	A	-	-	rs111475924		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62618328delA	uc001dab.2	+						INADL_uc001dac.2_Intron|INADL_uc009wag.2_Intron	NM_176877	NP_795352			InaD-like						intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	62882046	62882046	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62882046delT								KANK4 (96963 upstream) : USP1 (19929 downstream)																																			---	---	---	---
ATG4C	84938	broad.mit.edu	37	1	63304903	63304903	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63304903delT	uc001dat.2	+						ATG4C_uc001dau.2_Intron	NM_178221	NP_835739			APG4 autophagy 4 homolog C isoform 8						autophagic vacuole assembly|protein targeting to membrane|proteolysis	cytosol|extracellular region	cysteine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
ITGB3BP	23421	broad.mit.edu	37	1	63941842	63941842	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63941842delT	uc001dba.1	-						ITGB3BP_uc001dbb.1_Intron|ITGB3BP_uc001dbc.1_Intron|ITGB3BP_uc001dbd.1_Intron|ITGB3BP_uc009wak.1_Intron	NM_014288	NP_055103			integrin beta 3 binding protein						apoptosis|cell adhesion|CenH3-containing nucleosome assembly at centromere|induction of apoptosis by extracellular signals|mitotic prometaphase|nerve growth factor receptor signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome, centromeric region|cytosol|membrane fraction|nucleoplasm	protein C-terminus binding|signal transducer activity				0																		---	---	---	---
ROR1	4919	broad.mit.edu	37	1	64340544	64340544	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64340544delT	uc001dbj.2	+						ROR1_uc001dbi.3_Intron	NM_005012	NP_005003			receptor tyrosine kinase-like orphan receptor 1						transmembrane receptor protein tyrosine kinase signaling pathway	cytoplasm|integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			ovary(6)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|central_nervous_system(1)|skin(1)|kidney(1)	19																		---	---	---	---
UBE2U	148581	broad.mit.edu	37	1	64704841	64704861	+	Intron	DEL	AAGAAGAAGAAGAAGAAGAAG	-	-	rs36057587		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64704841_64704861delAAGAAGAAGAAGAAGAAGAAG	uc001dbn.1	+							NM_152489	NP_689702			ubiquitin-conjugating enzyme E2U (putative)								ATP binding|protein binding|ubiquitin-protein ligase activity				0																		---	---	---	---
RAVER2	55225	broad.mit.edu	37	1	65208134	65208135	+	5'Flank	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65208134_65208135delAA	uc001dbs.1	+							NM_018211	NP_060681			ribonucleoprotein, PTB-binding 2							cytoplasm|nucleus	nucleotide binding|RNA binding			large_intestine(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	65595924	65595924	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65595924delT								MIR101-1 (71733 upstream) : AK3L1 (17308 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	65695219	65695219	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65695219delA								AK3L1 (2046 upstream) : DNAJC6 (24929 downstream)																																			---	---	---	---
LEPR	3953	broad.mit.edu	37	1	66084182	66084182	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66084182delT	uc001dci.2	+						LEPR_uc001dcg.2_Intron|LEPR_uc001dch.2_Intron|LEPR_uc009waq.2_Intron|LEPR_uc001dcj.2_Intron|LEPR_uc001dck.2_Intron	NM_002303	NP_002294			leptin receptor isoform 1						energy reserve metabolic process|multicellular organismal development	extracellular region|integral to membrane|plasma membrane	cytokine receptor activity			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	66243393	66243393	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66243393delT								LEPR (140573 upstream) : PDE4B (14800 downstream)																																			---	---	---	---
WDR78	79819	broad.mit.edu	37	1	67374968	67374969	+	Intron	INS	-	AC	AC	rs143570368	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67374968_67374969insAC	uc001dcx.2	-						WDR78_uc001dcy.2_Intron|WDR78_uc001dcz.2_Intron	NM_024763	NP_079039			WD repeat domain 78 isoform 1											ovary(2)	2																		---	---	---	---
IL12RB2	3595	broad.mit.edu	37	1	67785887	67785887	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67785887delT	uc001ddu.2	+						IL12RB2_uc010oqi.1_Intron|IL12RB2_uc010oqj.1_Intron|IL12RB2_uc010oqk.1_5'Flank|IL12RB2_uc010oql.1_5'Flank|IL12RB2_uc010oqm.1_5'Flank|IL12RB2_uc010oqn.1_5'Flank	NM_001559	NP_001550			interleukin 12 receptor, beta 2 precursor						positive regulation of cell proliferation|positive regulation of interferon-gamma production	integral to plasma membrane	cytokine receptor activity			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	67907096	67907096	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67907096delA								SERBP1 (10973 upstream) : GADD45A (243787 downstream)																																			---	---	---	---
WLS	79971	broad.mit.edu	37	1	68600811	68600815	+	Intron	DEL	TTTCT	-	-	rs67054883		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68600811_68600815delTTTCT	uc001def.1	-						uc001deb.1_Intron|uc001dec.1_Intron|WLS_uc001dee.2_Intron|WLS_uc001deg.1_Intron|WLS_uc009wbf.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																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	68732613	68732613	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68732613delT								WLS (34360 upstream) : RPE65 (161894 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	69116256	69116257	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:69116256_69116257delTT								DEPDC1 (153457 upstream) : LRRC7 (916611 downstream)																																			---	---	---	---
LRRC7	57554	broad.mit.edu	37	1	70135429	70135429	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70135429delT	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	70470709	70470709	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70470709delT	uc001dep.2	+						LRRC7_uc009wbg.2_Intron	NM_020794	NP_065845			leucine rich repeat containing 7							centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14																		---	---	---	---
LRRC7	57554	broad.mit.edu	37	1	70482226	70482226	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70482226delT	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	70788677	70788678	+	Intron	DEL	AA	-	-	rs80136257		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70788677_70788678delAA	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	71854255	71854255	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:71854255delA								ZRANB2 (307510 upstream) : NEGR1 (14371 downstream)																																			---	---	---	---
NEGR1	257194	broad.mit.edu	37	1	72041939	72041939	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:72041939delT	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	73060450	73060450	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:73060450delA								NEGR1 (312045 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	73776570	73776571	+	RNA	INS	-	AG	AG	rs140930533	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:73776570_73776571insAG	uc001dfx.2	+	3		c.336_337insAG								Homo sapiens cDNA clone IMAGE:5272066.																														---	---	---	---
TNNI3K	51086	broad.mit.edu	37	1	74732937	74732937	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74732937delT	uc001dgf.1	+						TNNI3K_uc001dgc.1_Intron|TNNI3K_uc001dgd.2_Intron|TNNI3K_uc001dge.1_Intron	NM_015978	NP_057062			TNNI3 interacting kinase isoform b							cytoplasm|nucleus	ATP binding|metal ion binding|protein C-terminus binding|protein serine/threonine kinase activity|troponin I binding			large_intestine(4)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	10																		---	---	---	---
SLC44A5	204962	broad.mit.edu	37	1	75673354	75673354	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75673354delT	uc001dgu.2	-						SLC44A5_uc001dgt.2_Intron|SLC44A5_uc001dgs.2_Intron|SLC44A5_uc001dgr.2_Intron|SLC44A5_uc010oqz.1_Intron|SLC44A5_uc010ora.1_Intron|SLC44A5_uc010orb.1_Intron	NM_152697	NP_689910			solute carrier family 44, member 5 isoform A							integral to membrane|plasma membrane	choline transmembrane transporter activity			ovary(2)|skin(2)	4																		---	---	---	---
MSH4	4438	broad.mit.edu	37	1	76288497	76288497	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76288497delT	uc001dhd.1	+							NM_002440	NP_002431			mutS homolog 4						chiasma assembly|homologous chromosome segregation|mismatch repair|reciprocal meiotic recombination	synaptonemal complex	ATP binding|DNA-dependent ATPase activity|mismatched DNA binding			lung(3)|ovary(2)	5													MMR					---	---	---	---
MSH4	4438	broad.mit.edu	37	1	76370203	76370204	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76370203_76370204delTT	uc001dhd.1	+							NM_002440	NP_002431			mutS homolog 4						chiasma assembly|homologous chromosome segregation|mismatch repair|reciprocal meiotic recombination	synaptonemal complex	ATP binding|DNA-dependent ATPase activity|mismatched DNA binding			lung(3)|ovary(2)	5													MMR					---	---	---	---
Unknown	0	broad.mit.edu	37	1	76434525	76434526	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76434525_76434526insT								ASB17 (36409 upstream) : ST6GALNAC3 (105863 downstream)																																			---	---	---	---
ST6GALNAC3	256435	broad.mit.edu	37	1	76579214	76579214	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76579214delT	uc001dhh.2	+						ST6GALNAC3_uc001dhg.3_Intron|ST6GALNAC3_uc010orh.1_Intron	NM_152996	NP_694541			sialyltransferase 7C isoform 1						protein glycosylation	integral to Golgi membrane	sialyltransferase activity			ovary(3)|skin(2)	5																		---	---	---	---
ST6GALNAC3	256435	broad.mit.edu	37	1	76716779	76716779	+	Intron	DEL	T	-	-	rs140417921	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76716779delT	uc001dhh.2	+						ST6GALNAC3_uc001dhg.3_Intron|ST6GALNAC3_uc010orh.1_Intron	NM_152996	NP_694541			sialyltransferase 7C isoform 1						protein glycosylation	integral to Golgi membrane	sialyltransferase activity			ovary(3)|skin(2)	5																		---	---	---	---
AK5	26289	broad.mit.edu	37	1	77908550	77908551	+	Intron	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77908550_77908551delAG	uc001dhn.2	+						AK5_uc001dho.2_Intron	NM_174858	NP_777283			adenylate kinase 5 isoform 1						ADP biosynthetic process|ATP metabolic process|dADP biosynthetic process|nucleobase, nucleoside and nucleotide interconversion|pyrimidine ribonucleotide biosynthetic process|signal transduction	centrosome|cytosol	adenylate kinase activity|ATP binding|cAMP-dependent protein kinase regulator activity|nucleoside kinase activity			skin(1)	1																		---	---	---	---
ZZZ3	26009	broad.mit.edu	37	1	78052944	78052950	+	Intron	DEL	TTTTTTT	-	-	rs67865779		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78052944_78052950delTTTTTTT	uc001dhq.2	-						ZZZ3_uc001dhr.2_Intron|ZZZ3_uc009wbz.1_Intron|ZZZ3_uc001dhp.2_Intron	NM_015534	NP_056349			zinc finger, ZZ-type containing 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|large_intestine(1)	5																		---	---	---	---
MGC27382	149047	broad.mit.edu	37	1	78791912	78791913	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78791912_78791913delTT	uc009wcc.2	+							NR_027310				Homo sapiens cDNA FLJ34438 fis, clone HLUNG2001144.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	79801858	79801858	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79801858delC								ELTD1 (329363 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	80450593	80450594	+	IGR	INS	-	CTTAA	CTTAA	rs145108545	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:80450593_80450594insCTTAA								ELTD1 (978098 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	81180541	81180541	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:81180541delT								None (None upstream) : LPHN2 (591304 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	81439654	81439655	+	IGR	INS	-	A	A	rs79036535		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:81439654_81439655insA								None (None upstream) : LPHN2 (332190 downstream)																																			---	---	---	---
LPHN2	23266	broad.mit.edu	37	1	81953330	81953331	+	Intron	DEL	AA	-	-	rs66680509		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:81953330_81953331delAA	uc001dis.2	+											SubName: Full=cDNA FLJ41428 fis, clone BRHIP2005236, highly similar to Latrophilin-2;						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(3)|lung(3)|breast(2)|central_nervous_system(1)	9				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)														---	---	---	---
LPHN2	23266	broad.mit.edu	37	1	81999064	81999064	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:81999064delA	uc001dis.2	+											SubName: Full=cDNA FLJ41428 fis, clone BRHIP2005236, highly similar to Latrophilin-2;						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(3)|lung(3)|breast(2)|central_nervous_system(1)	9				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	83306496	83306501	+	IGR	DEL	ACACAC	-	-	rs113261979		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:83306496_83306501delACACAC								LPHN2 (848390 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	83513560	83513560	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:83513560delT								None (None upstream) : TTLL7 (821499 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	84709900	84709900	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84709900delA								PRKACB (5721 upstream) : SAMD13 (54149 downstream)																																			---	---	---	---
SSX2IP	117178	broad.mit.edu	37	1	85152670	85152670	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85152670delA	uc001dkh.2	-						SSX2IP_uc001dkg.2_Intron|SSX2IP_uc010orz.1_Intron|SSX2IP_uc001dki.2_Intron|SSX2IP_uc010osa.1_Intron|SSX2IP_uc001dkj.2_Intron|SSX2IP_uc009wci.2_Intron|SSX2IP_uc001dkk.1_Intron	NM_014021	NP_054740			synovial sarcoma, X breakpoint 2 interacting						cell adhesion	nucleus|protein complex				ovary(2)	2				all cancers(265;0.0053)|Epithelial(280;0.0214)|OV - Ovarian serous cystadenocarcinoma(397;0.173)														---	---	---	---
LPAR3	23566	broad.mit.edu	37	1	85360640	85360640	+	5'Flank	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85360640delA	uc009wcj.1	-							NM_012152	NP_036284			lysophosphatidic acid receptor 3						G-protein signaling, coupled to cyclic nucleotide second messenger|synaptic transmission	integral to plasma membrane|intracellular membrane-bounded organelle				lung(3)|ovary(2)	5																		---	---	---	---
SYDE2	84144	broad.mit.edu	37	1	85624415	85624415	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85624415delA	uc009wcm.2	-	7						NM_032184	NP_115560			synapse defective 1, Rho GTPase, homolog 2						activation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	Rho GTPase activator activity			ovary(1)|central_nervous_system(1)	2				all cancers(265;0.0126)|Epithelial(280;0.0336)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	87318084	87318085	+	IGR	DEL	TT	-	-	rs113913153		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87318084_87318085delTT								SH3GLB1 (104218 upstream) : SEP15 (10045 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	87844177	87844177	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87844177delT								LMO4 (29574 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	87938429	87938430	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87938429_87938430insA								LMO4 (123826 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	88229741	88229744	+	IGR	DEL	TTCT	-	-	rs111901367		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88229741_88229744delTTCT								LMO4 (415138 upstream) : PKN2 (920178 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	88346442	88346443	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88346442_88346443delTT								LMO4 (531839 upstream) : PKN2 (803479 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	88513636	88513636	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88513636delT								LMO4 (699033 upstream) : PKN2 (636286 downstream)																																			---	---	---	---
GBP5	115362	broad.mit.edu	37	1	89732904	89732904	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89732904delC	uc001dnc.2	-						GBP5_uc001dnd.2_Intron|GBP5_uc001dne.1_Intron	NM_052942	NP_443174			guanylate-binding protein 5							plasma membrane	GTP binding|GTPase activity			ovary(1)	1				all cancers(265;0.00784)|Epithelial(280;0.0286)														---	---	---	---
LRRC8C	84230	broad.mit.edu	37	1	90172965	90172965	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90172965delA	uc001dnl.3	+							NM_032270	NP_115646			leucine rich repeat containing 8 family, member							endoplasmic reticulum membrane|integral to membrane				ovary(3)|skin(3)|pancreas(1)|central_nervous_system(1)	8		all_lung(203;0.126)		all cancers(265;0.00756)|Epithelial(280;0.0313)														---	---	---	---
ZNF326	284695	broad.mit.edu	37	1	90482859	90482859	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90482859delT	uc001dnq.2	+						ZNF326_uc009wda.1_Intron|ZNF326_uc001dnr.2_Intron	NM_182976	NP_892021			zinc finger protein 326 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear matrix	DNA binding			ovary(1)	1		all_lung(203;0.0116)|Lung NSC(277;0.0417)		all cancers(265;0.00728)|Epithelial(280;0.0265)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	90981981	90981982	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90981981_90981982delAC								ZNF326 (487887 upstream) : BARHL2 (195598 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	91160493	91160494	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91160493_91160494insA								ZNF326 (666399 upstream) : BARHL2 (17086 downstream)																																			---	---	---	---
ZNF644	84146	broad.mit.edu	37	1	91485776	91485777	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91485776_91485777insA	uc001dnw.2	-						ZNF644_uc001dnv.2_Intron|ZNF644_uc001dnx.2_Intron|ZNF644_uc001dny.1_Intron	NM_201269	NP_958357			zinc finger protein 644 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	91721623	91721623	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91721623delA								ZNF644 (233952 upstream) : HFM1 (4701 downstream)																																			---	---	---	---
BRDT	676	broad.mit.edu	37	1	92433854	92433854	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92433854delT	uc001dok.3	+						BRDT_uc001dol.3_Intron|BRDT_uc010osz.1_Intron|BRDT_uc009wdf.2_Intron|BRDT_uc010ota.1_Intron|BRDT_uc010otb.1_Intron|BRDT_uc001dom.3_Intron	NM_207189	NP_997072			testis-specific bromodomain protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein serine/threonine kinase activity|transcription coactivator activity			stomach(2)|ovary(1)|lung(1)	4		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)														---	---	---	---
BRDT	676	broad.mit.edu	37	1	92447354	92447354	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92447354delT	uc001dok.3	+						BRDT_uc001dol.3_Intron|BRDT_uc010osz.1_Intron|BRDT_uc009wdf.2_Intron|BRDT_uc010ota.1_Intron|BRDT_uc010otb.1_Intron|BRDT_uc001dom.3_Intron	NM_207189	NP_997072			testis-specific bromodomain protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein serine/threonine kinase activity|transcription coactivator activity			stomach(2)|ovary(1)|lung(1)	4		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)														---	---	---	---
BRDT	676	broad.mit.edu	37	1	92467930	92467930	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92467930delT	uc001dok.3	+						BRDT_uc001dol.3_Intron|BRDT_uc010osz.1_Intron|BRDT_uc009wdf.2_Intron|BRDT_uc010ota.1_Intron|BRDT_uc010otb.1_Intron|BRDT_uc001dom.3_Intron	NM_207189	NP_997072			testis-specific bromodomain protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein serine/threonine kinase activity|transcription coactivator activity			stomach(2)|ovary(1)|lung(1)	4		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)														---	---	---	---
EPHX4	253152	broad.mit.edu	37	1	92525416	92525416	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92525416delT	uc001don.2	+							NM_173567	NP_775838			abhydrolase domain containing 7							integral to membrane	hydrolase activity			central_nervous_system(1)	1																		---	---	---	---
GLMN	11146	broad.mit.edu	37	1	92740654	92740654	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92740654delC	uc001dor.2	-						GLMN_uc009wdg.2_Intron|GLMN_uc001dos.2_Intron	NM_053274	NP_444504			glomulin						muscle cell differentiation|negative regulation of T cell proliferation|positive regulation of cytokine secretion|positive regulation of interleukin-2 biosynthetic process|positive regulation of phosphorylation|regulation of gene expression, epigenetic|vasculogenesis	intracellular	hepatocyte growth factor receptor binding			skin(1)	1		all_lung(203;0.00827)|Lung NSC(277;0.0295)		all cancers(265;0.00702)|GBM - Glioblastoma multiforme(16;0.0381)|Epithelial(280;0.0989)										Multiple_Glomus_Tumors_(of_the_Skin)_Familial				---	---	---	---
Unknown	0	broad.mit.edu	37	1	93288726	93288726	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93288726delA								EVI5 (30765 upstream) : RPL5 (8868 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	93489380	93489381	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93489380_93489381delTG								FAM69A (62301 upstream) : MTF2 (55411 downstream)																																			---	---	---	---
MTF2	22823	broad.mit.edu	37	1	93571239	93571239	+	Intron	DEL	T	-	-	rs3066510		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93571239delT	uc009wdj.2	+						MTF2_uc001dph.2_Intron|MTF2_uc010oth.1_Intron|MTF2_uc009wdk.2_Intron|MTF2_uc001dpi.3_Intron|MTF2_uc010oti.1_Intron|MTF2_uc001dpj.3_Intron	NM_007358	NP_031384			metal response element binding transcription							nucleus	DNA binding|zinc ion binding			ovary(2)	2		all_lung(203;0.00196)|Lung NSC(277;0.00902)|Melanoma(281;0.099)|Ovarian(761;0.109)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00076)|GBM - Glioblastoma multiforme(16;0.00157)|Epithelial(280;0.0886)														---	---	---	---
BCAR3	8412	broad.mit.edu	37	1	94037058	94037058	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94037058delA	uc001dpz.2	-						BCAR3_uc001dqa.2_Intron|BCAR3_uc001dqb.2_Intron|BCAR3_uc001dpx.3_Intron|BCAR3_uc001dpy.2_Intron|BCAR3_uc009wdm.1_3'UTR	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)														---	---	---	---
ABCA4	24	broad.mit.edu	37	1	94470795	94470795	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94470795delT	uc001dqh.2	-						ABCA4_uc001dqi.1_Intron	NM_000350	NP_000341			ATP-binding cassette, sub-family A member 4						phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)|skin(4)|central_nervous_system(2)|upper_aerodigestive_tract(1)|breast(1)	12		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)														---	---	---	---
RWDD3	25950	broad.mit.edu	37	1	95706405	95706405	+	Intron	DEL	A	-	-	rs113157057		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95706405delA	uc009wdu.2	+						RWDD3_uc001drd.3_Intron|RWDD3_uc010oty.1_Intron|RWDD3_uc009wdt.2_Intron|RWDD3_uc001drf.3_Intron|RWDD3_uc001drh.3_Intron|RWDD3_uc009wdv.2_Intron|RWDD3_uc001drg.3_Intron|RWDD3_uc001dri.3_Intron	NM_015485	NP_056300			RWD domain containing 3 isoform a							cytoplasm|nucleus	protein binding			ovary(1)	1		all_epithelial(167;5.99e-05)|all_lung(203;0.00168)|Lung NSC(277;0.00769)		all cancers(265;0.112)|Epithelial(280;0.229)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	96775018	96775018	+	IGR	DEL	T	-	-	rs35194073		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96775018delT								None (None upstream) : PTBP2 (412157 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	96884031	96884031	+	IGR	DEL	A	-	-	rs77096023		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96884031delA								None (None upstream) : PTBP2 (303144 downstream)																																			---	---	---	---
PTBP2	58155	broad.mit.edu	37	1	97186163	97186163	+	5'Flank	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97186163delA	uc001drq.2	+						PTBP2_uc001drn.2_5'Flank|PTBP2_uc001dro.2_5'Flank|PTBP2_uc010otz.1_5'Flank|PTBP2_uc001drp.2_5'Flank|PTBP2_uc009wdw.2_5'Flank|PTBP2_uc001drr.2_5'Flank|PTBP2_uc010oua.1_5'Flank|PTBP2_uc001dru.2_5'Flank|PTBP2_uc001drm.2_5'Flank	NM_021190	NP_067013			polypyrimidine tract binding protein 2								nucleotide binding				0		all_epithelial(167;2.95e-05)|all_lung(203;0.000396)|Lung NSC(277;0.00171)		all cancers(265;0.0582)|Epithelial(280;0.0716)|Colorectal(170;0.0879)|KIRC - Kidney renal clear cell carcinoma(1967;0.202)														---	---	---	---
PTBP2	58155	broad.mit.edu	37	1	97207227	97207227	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97207227delA	uc001drq.2	+						PTBP2_uc001drn.2_Intron|PTBP2_uc001dro.2_Intron|PTBP2_uc010otz.1_Intron|PTBP2_uc001drp.2_Intron|PTBP2_uc009wdw.2_Intron|PTBP2_uc001drr.2_Intron|PTBP2_uc010oua.1_Intron|PTBP2_uc001dru.2_Intron|PTBP2_uc001drm.2_Intron	NM_021190	NP_067013			polypyrimidine tract binding protein 2								nucleotide binding				0		all_epithelial(167;2.95e-05)|all_lung(203;0.000396)|Lung NSC(277;0.00171)		all cancers(265;0.0582)|Epithelial(280;0.0716)|Colorectal(170;0.0879)|KIRC - Kidney renal clear cell carcinoma(1967;0.202)														---	---	---	---
DPYD	1806	broad.mit.edu	37	1	97696136	97696136	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97696136delA	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	97734705	97734705	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97734705delT	uc001drv.2	-							NM_000110	NP_000101			dihydropyrimidine dehydrogenase isoform 1						'de novo' pyrimidine base biosynthetic process|purine base catabolic process|thymidine catabolic process|thymine catabolic process|UMP biosynthetic process|uracil catabolic process	cytosol	4 iron, 4 sulfur cluster binding|dihydroorotate oxidase activity|dihydropyrimidine dehydrogenase (NADP+) activity|electron carrier activity|flavin adenine dinucleotide binding|metal ion binding|NADP binding|protein homodimerization activity			ovary(3)|skin(3)|breast(2)	8		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Enfuvirtide(DB00109)													---	---	---	---
DPYD	1806	broad.mit.edu	37	1	98060470	98060470	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98060470delT	uc001drv.2	-							NM_000110	NP_000101			dihydropyrimidine dehydrogenase isoform 1						'de novo' pyrimidine base biosynthetic process|purine base catabolic process|thymidine catabolic process|thymine catabolic process|UMP biosynthetic process|uracil catabolic process	cytosol	4 iron, 4 sulfur cluster binding|dihydroorotate oxidase activity|dihydropyrimidine dehydrogenase (NADP+) activity|electron carrier activity|flavin adenine dinucleotide binding|metal ion binding|NADP binding|protein homodimerization activity			ovary(3)|skin(3)|breast(2)	8		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Enfuvirtide(DB00109)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	98831642	98831643	+	IGR	DEL	AT	-	-	rs72195149	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98831642_98831643delAT								MIR137 (319915 upstream) : SNX7 (295593 downstream)																																			---	---	---	---
LPPR4	9890	broad.mit.edu	37	1	99758338	99758338	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99758338delT	uc001dse.2	+						LPPR4_uc010oue.1_Intron	NM_014839	NP_055654			plasticity related gene 1								phosphatidate phosphatase activity			ovary(3)	3		all_epithelial(167;3.54e-06)|all_lung(203;0.00139)|Lung NSC(277;0.00202)		Epithelial(280;0.0736)|all cancers(265;0.0975)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)|Colorectal(170;0.22)														---	---	---	---
SASS6	163786	broad.mit.edu	37	1	100572825	100572825	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100572825delA	uc001dsu.2	-						SASS6_uc009wdz.2_Intron	NM_194292	NP_919268			spindle assembly abnormal protein 6						centriole replication	centriole				upper_aerodigestive_tract(1)|ovary(1)	2		all_epithelial(167;4.58e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.085)|all cancers(265;0.139)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.197)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	101093401	101093402	+	IGR	INS	-	T	T	rs141056982	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101093401_101093402insT								GPR88 (85819 upstream) : VCAM1 (91895 downstream)																																			---	---	---	---
OLFM3	118427	broad.mit.edu	37	1	102358807	102358807	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102358807delA	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)														---	---	---	---
OLFM3	118427	broad.mit.edu	37	1	102400204	102400204	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102400204delA	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)														---	---	---	---
OLFM3	118427	broad.mit.edu	37	1	102400869	102400870	+	Intron	INS	-	A	A	rs112998272		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102400869_102400870insA	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	104689282	104689283	+	IGR	INS	-	A	A	rs141602495	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104689282_104689283insA								AMY1A (482110 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	105293853	105293853	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:105293853delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	105708757	105708757	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:105708757delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	106027093	106027093	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:106027093delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	106346799	106346799	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:106346799delC								None (None upstream) : None (None downstream)																																			---	---	---	---
NTNG1	22854	broad.mit.edu	37	1	107691083	107691083	+	5'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107691083delA	uc001dvh.3	+	2					NTNG1_uc001dvf.3_5'UTR|NTNG1_uc010out.1_5'UTR|NTNG1_uc001dvc.3_5'UTR|NTNG1_uc001dvd.1_5'UTR	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	107805968	107805968	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107805968delT	uc001dvh.3	+						NTNG1_uc001dvf.3_Intron|NTNG1_uc010out.1_Intron|NTNG1_uc001dvc.3_Intron|NTNG1_uc001dvd.1_Intron	NM_001113226	NP_001106697			netrin G1 isoform 1						axonogenesis	anchored to plasma membrane	protein binding			large_intestine(2)|ovary(2)|skin(2)	6		all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243)		Lung(183;0.0946)|BRCA - Breast invasive adenocarcinoma(282;0.237)|Epithelial(280;0.245)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	108033373	108033374	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108033373_108033374insT								NTNG1 (8902 upstream) : VAV3 (80408 downstream)																																			---	---	---	---
VAV3	10451	broad.mit.edu	37	1	108269174	108269176	+	Intron	DEL	CTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108269174_108269176delCTT	uc001dvk.1	-						VAV3_uc010ouw.1_Intron|VAV3_uc001dvl.1_Intron|VAV3_uc010oux.1_Intron	NM_006113	NP_006104			vav 3 guanine nucleotide exchange factor isoform						angiogenesis|apoptosis|B cell receptor signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of B cell proliferation|regulation of Rho protein signal transduction|response to DNA damage stimulus|response to drug|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(5)|lung(2)|breast(2)	9		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	108865941	108865942	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108865941_108865942delTT								NBPF4 (79238 upstream) : NBPF6 (126962 downstream)																																			---	---	---	---
FAM102B	284611	broad.mit.edu	37	1	109136603	109136603	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109136603delT	uc010ouy.1	+							NM_001010883	NP_001010883			hypothetical protein LOC284611											large_intestine(1)	1		all_epithelial(167;5.52e-05)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0217)|Lung(183;0.109)|COAD - Colon adenocarcinoma(174;0.141)|Epithelial(280;0.182)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	109355030	109355030	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109355030delA								STXBP3 (2891 upstream) : AKNAD1 (3502 downstream)																																			---	---	---	---
WDR47	22911	broad.mit.edu	37	1	109514411	109514412	+	Intron	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109514411_109514412delCT	uc001dwj.2	-						WDR47_uc001dwl.2_Intron|WDR47_uc001dwi.2_Intron|WDR47_uc010ovf.1_Intron	NM_001142551	NP_001136023			WD repeat domain 47 isoform 3											ovary(1)	1		all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822)		Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244)														---	---	---	---
WDR47	22911	broad.mit.edu	37	1	109538079	109538079	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109538079delA	uc001dwj.2	-						WDR47_uc001dwl.2_Intron|WDR47_uc001dwi.2_Intron|WDR47_uc001dwk.2_Intron|WDR47_uc010ovf.1_Intron	NM_001142551	NP_001136023			WD repeat domain 47 isoform 3											ovary(1)	1		all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822)		Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244)														---	---	---	---
KIAA1324	57535	broad.mit.edu	37	1	109656729	109656729	+	5'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109656729delT	uc001dwq.2	+	2					KIAA1324_uc009wex.1_5'UTR|KIAA1324_uc009wey.2_5'UTR|KIAA1324_uc010ovg.1_5'UTR|C1orf194_uc009wev.2_5'Flank|C1orf194_uc001dwp.3_5'Flank|C1orf194_uc009wew.2_5'Flank	NM_020775	NP_065826			hypothetical protein LOC57535 precursor						macroautophagy|positive regulation of vacuole organization|regulation of apoptosis	integral to plasma membrane				ovary(2)|haematopoietic_and_lymphoid_tissue(1)|breast(1)|skin(1)	5		all_epithelial(167;0.000102)|all_lung(203;0.000323)|Lung NSC(277;0.00063)		Colorectal(144;0.0188)|Lung(183;0.0527)|COAD - Colon adenocarcinoma(174;0.14)|Epithelial(280;0.21)|all cancers(265;0.249)														---	---	---	---
KIAA1324	57535	broad.mit.edu	37	1	109714174	109714174	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109714174delA	uc001dwq.2	+						KIAA1324_uc009wex.1_Intron|KIAA1324_uc009wey.2_Intron|KIAA1324_uc010ovg.1_Intron	NM_020775	NP_065826			hypothetical protein LOC57535 precursor						macroautophagy|positive regulation of vacuole organization|regulation of apoptosis	integral to plasma membrane				ovary(2)|haematopoietic_and_lymphoid_tissue(1)|breast(1)|skin(1)	5		all_epithelial(167;0.000102)|all_lung(203;0.000323)|Lung NSC(277;0.00063)		Colorectal(144;0.0188)|Lung(183;0.0527)|COAD - Colon adenocarcinoma(174;0.14)|Epithelial(280;0.21)|all cancers(265;0.249)														---	---	---	---
SARS	6301	broad.mit.edu	37	1	109772796	109772796	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109772796delA	uc001dwu.1	+						SARS_uc001dwt.1_Intron|SARS_uc001dwv.1_Intron|SARS_uc001dww.1_Intron|SARS_uc001dwx.1_Intron|SARS_uc009wfa.1_Intron|SARS_uc001dwy.1_Intron|SARS_uc001dwz.1_Intron	NM_006513	NP_006504			seryl-tRNA synthetase						seryl-tRNA aminoacylation|tRNA processing	cytosol	ATP binding|protein binding|RNA binding|serine-tRNA ligase activity			central_nervous_system(1)	1		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0301)|Lung(183;0.0677)|COAD - Colon adenocarcinoma(174;0.116)|Epithelial(280;0.233)	L-Serine(DB00133)													---	---	---	---
CELSR2	1952	broad.mit.edu	37	1	109794993	109794993	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109794993delG	uc001dxa.3	+	1	2353	c.2292delG	c.(2290-2292)ACGfs	p.T764fs		NM_001408	NP_001399	Q9HCU4	CELR2_HUMAN	cadherin EGF LAG seven-pass G-type receptor 2	764	Cadherin 6.|Extracellular (Potential).				dendrite morphogenesis|homophilic cell adhesion|neural plate anterior/posterior regionalization|neuropeptide signaling pathway|regulation of cell-cell adhesion|regulation of transcription, DNA-dependent|Wnt receptor signaling pathway	cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(4)|lung(3)|skin(1)	8		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)														---	---	---	---
MYBPHL	343263	broad.mit.edu	37	1	109836686	109836686	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109836686delA	uc001dxk.1	-						MYBPHL_uc010ovh.1_Intron|MYBPHL_uc001dxl.2_Intron	NM_001010985	NP_001010985			myosin binding protein H-like											ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_lung(203;0.00519)|all_epithelial(167;0.00575)|Lung NSC(277;0.00822)		Colorectal(144;0.0306)|Lung(183;0.0681)|COAD - Colon adenocarcinoma(174;0.117)|Epithelial(280;0.197)|all cancers(265;0.225)														---	---	---	---
SYPL2	284612	broad.mit.edu	37	1	110012123	110012123	+	Intron	DEL	A	-	-	rs1368988	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110012123delA	uc001dxp.2	+						SYPL2_uc001dxo.2_Intron|SYPL2_uc010ovk.1_Intron	NM_001040709	NP_001035799			mitsugumin 29							integral to membrane|synaptic vesicle	transporter activity			ovary(1)	1		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Colorectal(144;0.0129)|Lung(183;0.0436)|READ - Rectum adenocarcinoma(129;0.0698)|Epithelial(280;0.0808)|all cancers(265;0.0869)|LUSC - Lung squamous cell carcinoma(189;0.231)														---	---	---	---
AHCYL1	10768	broad.mit.edu	37	1	110555139	110555140	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110555139_110555140delTT	uc001dyx.2	+						AHCYL1_uc010ovw.1_Intron|AHCYL1_uc001dyy.2_Intron|AHCYL1_uc010ovx.1_Intron	NM_006621	NP_006612			S-adenosylhomocysteine hydrolase-like 1						one-carbon metabolic process	endoplasmic reticulum	adenosylhomocysteinase activity			ovary(1)	1		all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0259)|Colorectal(144;0.123)|all cancers(265;0.134)|Epithelial(280;0.141)|LUSC - Lung squamous cell carcinoma(189;0.143)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	110689243	110689243	+	IGR	DEL	G	-	-	rs35629821		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110689243delG								UBL4B (32675 upstream) : SLC6A17 (3889 downstream)																																			---	---	---	---
SLC16A4	9122	broad.mit.edu	37	1	110908782	110908782	+	Intron	DEL	T	-	-	rs72432884		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110908782delT	uc001dzo.1	-						SLC16A4_uc009wfs.1_Intron|SLC16A4_uc001dzp.1_Intron|SLC16A4_uc010ovy.1_Intron|SLC16A4_uc001dzq.1_Intron|SLC16A4_uc010ovz.1_Intron	NM_004696	NP_004687			solute carrier family 16, member 4							integral to plasma membrane|membrane fraction	monocarboxylic acid transmembrane transporter activity|symporter activity			ovary(3)	3		all_cancers(81;0.000476)|all_epithelial(167;0.000401)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0251)|all cancers(265;0.0766)|Epithelial(280;0.0807)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.14)	Pyruvic acid(DB00119)													---	---	---	---
SLC16A4	9122	broad.mit.edu	37	1	110934640	110934640	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110934640delT	uc001dzo.1	-						SLC16A4_uc009wfs.1_5'Flank|SLC16A4_uc001dzp.1_5'Flank|SLC16A4_uc010ovy.1_5'Flank|SLC16A4_uc001dzq.1_5'Flank|SLC16A4_uc010ovz.1_5'Flank	NM_004696	NP_004687			solute carrier family 16, member 4							integral to plasma membrane|membrane fraction	monocarboxylic acid transmembrane transporter activity|symporter activity			ovary(3)	3		all_cancers(81;0.000476)|all_epithelial(167;0.000401)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0251)|all cancers(265;0.0766)|Epithelial(280;0.0807)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.14)	Pyruvic acid(DB00119)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	111522357	111522358	+	IGR	DEL	TT	-	-	rs71950154		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111522357_111522358delTT								C1orf103 (15791 upstream) : DRAM2 (137597 downstream)																																			---	---	---	---
ADORA3	140	broad.mit.edu	37	1	112043544	112043544	+	Intron	DEL	T	-	-	rs66775324		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112043544delT	uc001ebh.3	-						ADORA3_uc001ebg.3_Intron|ADORA3_uc001ebf.2_Intron	NM_000677	NP_000668			adenosine A3 receptor isoform 2						activation of adenylate cyclase activity|inflammatory response|regulation of heart contraction	integral to plasma membrane	adenosine receptor activity, G-protein coupled			ovary(2)|large_intestine(1)|skin(1)	4		all_cancers(81;1.63e-06)|all_epithelial(167;5.01e-06)|all_lung(203;8.02e-05)|Lung NSC(277;0.000156)		all cancers(265;0.0185)|Colorectal(144;0.0186)|Lung(183;0.0238)|COAD - Colon adenocarcinoma(174;0.0644)|Epithelial(280;0.0872)|LUSC - Lung squamous cell carcinoma(189;0.134)	Adenosine(DB00640)|Aminophylline(DB01223)													---	---	---	---
KCND3	3752	broad.mit.edu	37	1	112336458	112336458	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112336458delA	uc001ebu.1	-						KCND3_uc001ebv.1_Intron	NM_004980	NP_004971			potassium voltage-gated channel, Shal-related							sarcolemma|voltage-gated potassium channel complex	A-type (transient outward) potassium channel activity|metal ion binding			ovary(2)|large_intestine(1)	3		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	112865714	112865714	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112865714delA								KCND3 (333937 upstream) : CTTNBP2NL (73086 downstream)																																			---	---	---	---
ST7L	54879	broad.mit.edu	37	1	113066621	113066621	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113066621delA	uc001ecd.2	-	15					ST7L_uc009wgh.2_RNA|ST7L_uc001ecc.2_3'UTR|ST7L_uc010owg.1_3'UTR|ST7L_uc010owh.1_3'UTR|ST7L_uc001ece.2_3'UTR|ST7L_uc001ecf.2_3'UTR|ST7L_uc001ecg.2_RNA	NM_017744	NP_060214			suppression of tumorigenicity 7-like isoform 1						negative regulation of cell growth	integral to membrane	binding				0	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
MOV10	4343	broad.mit.edu	37	1	113225544	113225545	+	Intron	DEL	TT	-	-	rs145655831		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113225544_113225545delTT	uc001eck.2	+						MOV10_uc001ecl.2_Intron|MOV10_uc001ecn.2_Intron|MOV10_uc001ecm.2_Intron|MOV10_uc009wgj.1_Intron	NM_001130079	NP_001123551			Mov10, Moloney leukemia virus 10, homolog						mRNA cleavage involved in gene silencing by miRNA|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body	ATP binding|helicase activity|protein binding|RNA binding			ovary(4)|skin(1)	5	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	113410448	113410448	+	IGR	DEL	T	-	-	rs7546769		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113410448delT								FAM19A3 (140594 upstream) : SLC16A1 (44024 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	113411278	113411279	+	IGR	INS	-	A	A	rs149523846	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113411278_113411279insA								FAM19A3 (141424 upstream) : SLC16A1 (43193 downstream)																																			---	---	---	---
LRIG2	9860	broad.mit.edu	37	1	113666350	113666351	+	Intron	DEL	TG	-	-	rs66524955		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113666350_113666351delTG	uc001edf.1	+						LRIG2_uc009wgn.1_Intron	NM_014813	NP_055628			leucine-rich repeats and immunoglobulin-like							cytoplasm|integral to membrane|plasma membrane				ovary(3)	3	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	113842487	113842487	+	IGR	DEL	C	-	-	rs36104089		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113842487delC								LRIG2 (175145 upstream) : MAGI3 (90988 downstream)																																			---	---	---	---
MAGI3	260425	broad.mit.edu	37	1	114021719	114021719	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114021719delC	uc001edk.2	+						MAGI3_uc001edh.3_Intron|MAGI3_uc001edi.3_Intron|MAGI3_uc010owm.1_Intron	NM_001142782	NP_001136254			membrane-associated guanylate kinase-related  3						apoptosis|interspecies interaction between organisms|intracellular signal transduction	nucleus|tight junction	ATP binding|guanylate kinase activity|protein binding			lung(3)|ovary(2)|central_nervous_system(1)	6	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
MAGI3	260425	broad.mit.edu	37	1	114123142	114123142	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114123142delT	uc001edk.2	+						MAGI3_uc001edh.3_Intron|MAGI3_uc001edi.3_Intron|MAGI3_uc010owm.1_Intron	NM_001142782	NP_001136254			membrane-associated guanylate kinase-related  3						apoptosis|interspecies interaction between organisms|intracellular signal transduction	nucleus|tight junction	ATP binding|guanylate kinase activity|protein binding			lung(3)|ovary(2)|central_nervous_system(1)	6	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
AMPD1	270	broad.mit.edu	37	1	115217930	115217930	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115217930delA	uc001efe.1	-						AMPD1_uc001eff.1_Intron	NM_000036	NP_000027			adenosine monophosphate deaminase 1 (isoform M)						purine base metabolic process|purine ribonucleoside monophosphate biosynthetic process|purine-containing compound salvage	cytosol	AMP deaminase activity|metal ion binding			ovary(2)|large_intestine(1)|skin(1)	4	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	Adenosine monophosphate(DB00131)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	115242691	115242691	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115242691delT								AMPD1 (4515 upstream) : NRAS (4388 downstream)																																			---	---	---	---
SYCP1	6847	broad.mit.edu	37	1	115455543	115455543	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115455543delT	uc001efr.2	+						SYCP1_uc010owt.1_Intron|SYCP1_uc001efq.2_Intron|SYCP1_uc009wgw.2_Intron	NM_003176	NP_003167			synaptonemal complex protein 1						cell division|reciprocal meiotic recombination|spermatogenesis|synaptonemal complex assembly		DNA binding			skin(1)	1	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	115781284	115781284	+	IGR	DEL	T	-	-	rs34537348		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115781284delT								TSPAN2 (149169 upstream) : NGF (47253 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	115893953	115893954	+	IGR	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115893953_115893954delGT								NGF (13096 upstream) : VANGL1 (290620 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	115997373	115997374	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115997373_115997374delAC								NGF (116516 upstream) : VANGL1 (187200 downstream)																																			---	---	---	---
CD2	914	broad.mit.edu	37	1	117302050	117302051	+	Intron	INS	-	A	A	rs66603322		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117302050_117302051insA	uc001egu.3	+						CD2_uc010owz.1_Intron|CD2_uc010oxa.1_Intron	NM_001767	NP_001758			CD2 molecule precursor						blood coagulation|cell surface receptor linked signaling pathway|cell-cell adhesion|induction of apoptosis|leukocyte migration|membrane raft polarization|natural killer cell activation|positive regulation of myeloid dendritic cell activation|regulation of T cell differentiation|T cell activation	integral to plasma membrane	receptor activity			breast(1)	1	Lung SC(450;0.225)	all_cancers(81;3.15e-06)|Acute lymphoblastic leukemia(138;1.7e-08)|all_epithelial(167;8.38e-07)|all_lung(203;3.37e-06)|Lung NSC(69;2.31e-05)		Epithelial(280;6.71e-26)|OV - Ovarian serous cystadenocarcinoma(397;4.74e-24)|all cancers(265;1.93e-22)|Lung(183;0.0543)|Kidney(133;0.0813)|Colorectal(144;0.174)|KIRC - Kidney renal clear cell carcinoma(1967;0.176)|LUSC - Lung squamous cell carcinoma(189;0.189)|BRCA - Breast invasive adenocarcinoma(282;0.201)	Alefacept(DB00092)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	117389501	117389502	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117389501_117389502insA								CD2 (77651 upstream) : PTGFRN (63187 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	118397274	118397274	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118397274delG								FAM46C (226264 upstream) : GDAP2 (8834 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	118846324	118846324	+	IGR	DEL	A	-	-	rs150282552	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118846324delA								SPAG17 (118476 upstream) : TBX15 (579342 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	119690806	119690806	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119690806delT	uc001ehp.1	+						uc001eho.1_Intron|uc009whk.1_Intron					Homo sapiens cDNA FLJ43771 fis, clone TESTI2049553.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	120010488	120010489	+	IGR	DEL	TA	-	-	rs4659179	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120010488_120010489delTA								HSD3B2 (21368 upstream) : HSD3B1 (39337 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	120227772	120227772	+	IGR	DEL	T	-	-	rs11361849		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120227772delT								ZNF697 (37382 upstream) : PHGDH (26647 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	120454043	120454043	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120454043delA								ADAM30 (14930 upstream) : NOTCH2 (135 downstream)																																			---	---	---	---
NOTCH2	4853	broad.mit.edu	37	1	120560007	120560008	+	Intron	INS	-	A	A	rs138352700	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120560007_120560008insA	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	142692134	142692134	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142692134delA	uc001eiw.1	+						uc001eix.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	143495919	143495920	+	IGR	INS	-	CTCAAC	CTCAAC	rs147646217	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143495919_143495920insCTCAAC								None (None upstream) : LOC100286793 (151719 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	144022637	144022640	+	Intron	DEL	TTCA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144022637_144022640delTTCA	uc010oxm.1	+											SubName: Full=Novel protein similar to SLIT-ROBO Rho GTPase activating protein 2 SRGAP2; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	144033055	144033056	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144033055_144033056delAA	uc010oxm.1	+											SubName: Full=Novel protein similar to SLIT-ROBO Rho GTPase activating protein 2 SRGAP2; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	144051162	144051162	+	Intron	DEL	T	-	-	rs77196483		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144051162delT	uc010oxm.1	+											SubName: Full=Novel protein similar to SLIT-ROBO Rho GTPase activating protein 2 SRGAP2; Flags: Fragment;																														---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	144529132	144529133	+	Intron	INS	-	G	G	rs75901853		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144529132_144529133insG	uc010oxr.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron	NM_001037675	NP_001032764			hypothetical protein LOC400818							cytoplasm					0																		---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	144597216	144597217	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144597216_144597217delTT	uc010oxr.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|NBPF9_uc010oye.1_Intron|uc001elc.2_RNA|NBPF9_uc009wif.1_Intron|uc001ele.2_Intron	NM_001037675	NP_001032764			hypothetical protein LOC400818							cytoplasm					0																		---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	144830505	144830506	+	Intron	DEL	GA	-	-	rs148464226	by1000genomes;by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144830505_144830506delGA	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron					RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0																		---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	144918474	144918477	+	Intron	DEL	GTTT	-	-	rs67298873		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144918474_144918477delGTTT	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								---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	145199593	145199594	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145199593_145199594delAC	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	145250342	145250342	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145250342delA	uc001emp.3	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NOTCH2NL_uc001emn.3_Intron|NOTCH2NL_uc001emm.3_Intron|NOTCH2NL_uc001emo.2_Intron|NOTCH2NL_uc010oyh.1_Intron	NM_017940	NP_060410			hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)														---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	145264368	145264368	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145264368delT	uc001emp.3	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NOTCH2NL_uc001emn.3_Intron|NOTCH2NL_uc001emm.3_Intron|NOTCH2NL_uc001emo.2_Intron|NOTCH2NL_uc010oyh.1_Intron	NM_017940	NP_060410			hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)														---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	145591854	145591855	+	Intron	DEL	AC	-	-	rs71885741		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145591854_145591855delAC	uc001emp.3	+						NUDT17_uc001eoe.2_5'Flank|NUDT17_uc001eof.1_5'Flank	NM_017940	NP_060410			hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)														---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	145824206	145824206	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145824206delA	uc001emp.3	+						GPR89A_uc010ozb.1_Intron|GPR89A_uc001eos.2_Intron|GPR89A_uc001eot.2_Intron|GPR89A_uc010ozc.1_Intron|GPR89A_uc010ozd.1_Intron|GPR89A_uc010oze.1_Intron	NM_017940	NP_060410			hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)														---	---	---	---
GPR89B	51463	broad.mit.edu	37	1	147408976	147408976	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147408976delA	uc001epv.3	+						GPR89B_uc010ozs.1_Intron|GPR89B_uc010ozt.1_Intron|GPR89B_uc010ozu.1_Intron|GPR89B_uc001epw.3_Intron|GPR89B_uc010ozv.1_Intron	NM_016334	NP_057418			G protein-coupled receptor 89B						intracellular pH reduction|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein transport	Golgi cisterna membrane|Golgi-associated vesicle membrane|integral to membrane	signal transducer activity|voltage-gated anion channel activity				0	all_hematologic(923;0.0276)																	---	---	---	---
LOC200030	200030	broad.mit.edu	37	1	148000700	148000700	+	Intron	DEL	T	-	-	rs67402181		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148000700delT	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	148849929	148849930	+	IGR	INS	-	TCATTTCA	TCATTTCA	rs141758216	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148849929_148849930insTCATTTCA								NBPF16 (91618 upstream) : LOC645166 (78356 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	148853741	148853741	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148853741delC								NBPF16 (95430 upstream) : LOC645166 (74545 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	149220947	149220947	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149220947delC								LOC645166 (267893 upstream) : LOC388692 (58529 downstream)																																			---	---	---	---
LOC388692	388692	broad.mit.edu	37	1	149281933	149281934	+	RNA	INS	-	AGT	AGT	rs150270984	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149281933_149281934insAGT	uc010pbf.1	+	1		c.2458_2459insAGT				NR_027002				Homo sapiens cDNA FLJ13580 fis, clone PLACE1008851.												0																		---	---	---	---
PRPF3	9129	broad.mit.edu	37	1	150297639	150297639	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150297639delA	uc001eum.3	+						PRPF3_uc009wlo.2_Intron|PRPF3_uc009wlp.2_Intron|PRPF3_uc010pca.1_Intron|PRPF3_uc010pcb.1_Intron	NM_004698	NP_004689			PRP3 pre-mRNA processing factor 3 homolog						nuclear mRNA splicing, via spliceosome	Cajal body|cytoplasm|nuclear speck|spliceosomal complex	protein binding			ovary(1)	1	Lung NSC(24;5.57e-29)|Breast(34;0.000844)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)	Colorectal(1306;0.0149)														---	---	---	---
RPRD2	23248	broad.mit.edu	37	1	150412447	150412447	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150412447delT	uc009wlr.2	+						RPRD2_uc010pcc.1_Intron|RPRD2_uc001eup.3_Intron	NM_015203	NP_056018			Regulation of nuclear pre-mRNA domain containing								protein binding			ovary(1)	1																		---	---	---	---
RPRD2	23248	broad.mit.edu	37	1	150428666	150428666	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150428666delT	uc009wlr.2	+						RPRD2_uc010pcc.1_Intron|RPRD2_uc001eup.3_Intron	NM_015203	NP_056018			Regulation of nuclear pre-mRNA domain containing								protein binding			ovary(1)	1																		---	---	---	---
BNIPL	149428	broad.mit.edu	37	1	151010862	151010862	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151010862delA	uc001ewl.2	+						BNIPL_uc009wmi.2_Intron|BNIPL_uc009wmj.2_5'Flank	NM_138278	NP_612122			BCL2/adenovirus E1B 19kD interacting protein						apoptosis|induction of apoptosis|negative regulation of cell proliferation|regulation of growth rate	cytosol|nucleus	identical protein binding				0	Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
SCNM1	79005	broad.mit.edu	37	1	151141072	151141073	+	Intron	INS	-	G	G	rs146855085	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151141072_151141073insG	uc001ewz.2	+						LYSMD1_uc001ewy.2_5'Flank|LYSMD1_uc010pcr.1_5'Flank|SCNM1_uc009wmn.2_Intron	NM_024041	NP_076946			sodium channel modifier 1						mRNA processing|RNA splicing	nucleus	metal ion binding|protein binding			upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|skin(1)	4	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	151247497	151247497	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151247497delA								PSMD4 (7545 upstream) : ZNF687 (6597 downstream)																																			---	---	---	---
TDRKH	11022	broad.mit.edu	37	1	151752311	151752311	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151752311delT	uc009wnb.1	-						TDRKH_uc001eyy.2_Intron|TDRKH_uc001ezb.3_Intron|TDRKH_uc001ezc.3_Intron|TDRKH_uc001eza.3_Intron|TDRKH_uc001ezd.3_Intron|TDRKH_uc010pdn.1_Intron	NM_006862	NP_006853			tudor and KH domain containing isoform a								RNA binding			ovary(1)|pancreas(1)	2	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
LINGO4	339398	broad.mit.edu	37	1	151777929	151777929	+	5'Flank	DEL	T	-	-	rs113064389		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151777929delT	uc001ezf.1	-							NM_001004432	NP_001004432			leucine rich repeat and Ig domain containing 4							integral to membrane				large_intestine(1)	1	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	152138299	152138299	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152138299delT								RPTN (6595 upstream) : HRNR (46259 downstream)																																			---	---	---	---
HRNR	388697	broad.mit.edu	37	1	152184857	152184857	+	3'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152184857delT	uc001ezt.1	-	3						NM_001009931	NP_001009931			hornerin						keratinization		calcium ion binding|protein binding			skin(2)|ovary(1)	3	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	152654065	152654068	+	IGR	DEL	ACAC	-	-	rs112460096		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152654065_152654068delACAC								LCE2C (5018 upstream) : LCE2B (4531 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	152952307	152952308	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152952307_152952308delTC								SPRR4 (7238 upstream) : SPRR1A (4249 downstream)																																			---	---	---	---
S100A3	6274	broad.mit.edu	37	1	153519823	153519823	+	3'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153519823delT	uc001fca.1	-	3					S100A4_uc001fby.2_5'Flank|S100A4_uc001fbz.2_5'Flank|uc009wog.1_Intron	NM_002960	NP_002951			S100 calcium binding protein A3								calcium ion binding|protein binding				0	all_lung(78;5.98e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	153758073	153758073	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153758073delT								SLC27A3 (5441 upstream) : GATAD2B (19131 downstream)																																			---	---	---	---
DENND4B	9909	broad.mit.edu	37	1	153911890	153911890	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153911890delC	uc001fdd.1	-							NM_014856	NP_055671			DENN/MADD domain containing 4B											ovary(1)	1	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)															---	---	---	---
NUP210L	91181	broad.mit.edu	37	1	154090122	154090122	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154090122delT	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)															---	---	---	---
UBAP2L	9898	broad.mit.edu	37	1	154194628	154194628	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154194628delT	uc001fep.3	+						C1orf43_uc001fei.2_5'Flank|C1orf43_uc001feg.2_5'Flank|C1orf43_uc001feh.2_5'Flank|C1orf43_uc001fej.2_5'Flank|C1orf43_uc009wos.1_5'Flank|C1orf43_uc001fek.2_5'Flank|C1orf43_uc001fel.2_5'Flank|UBAP2L_uc009wot.2_Intron|UBAP2L_uc010pek.1_Intron|UBAP2L_uc010pel.1_Intron|UBAP2L_uc001fen.1_Intron|UBAP2L_uc010pem.1_Intron	NM_014847	NP_055662			ubiquitin associated protein 2-like isoform a						binding of sperm to zona pellucida		protein binding			ovary(1)|central_nervous_system(1)	2	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	154875436	154875436	+	IGR	DEL	A	-	-	rs74746181		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154875436delA								KCNN3 (32682 upstream) : PMVK (21773 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	154890495	154890495	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154890495delA								KCNN3 (47741 upstream) : PMVK (6714 downstream)																																			---	---	---	---
FLAD1	80308	broad.mit.edu	37	1	154957881	154957884	+	Intron	DEL	TTTT	-	-	rs112698790		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154957881_154957884delTTTT	uc001fgf.1	+						FLAD1_uc001fgc.2_Intron|FLAD1_uc001fgd.1_Intron|FLAD1_uc001fge.1_Intron|FLAD1_uc001fgg.1_Intron|FLAD1_uc001fgh.1_5'Flank	NM_025207	NP_079483			flavin adenine dinucleotide synthetase isoform						FAD biosynthetic process|Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cytosol	ATP binding|FMN adenylyltransferase activity			ovary(2)|skin(1)	3	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)															---	---	---	---
ASH1L	55870	broad.mit.edu	37	1	155392743	155392743	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155392743delT	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)															---	---	---	---
KIAA0907	22889	broad.mit.edu	37	1	155884156	155884156	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155884156delA	uc001fmi.1	-						RIT1_uc001fmh.1_5'Flank|RIT1_uc010pgr.1_5'Flank|KIAA0907_uc001fmj.1_3'UTR|KIAA0907_uc009wrk.1_Intron	NM_014949	NP_055764			hypothetical protein LOC22889												0	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;8.82e-06)															---	---	---	---
KIAA0907	22889	broad.mit.edu	37	1	155886695	155886696	+	Intron	DEL	TT	-	-	rs113079820		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155886695_155886696delTT	uc001fmi.1	-						KIAA0907_uc001fmj.1_Intron|KIAA0907_uc009wrk.1_Intron|KIAA0907_uc009wrl.1_Intron	NM_014949	NP_055764			hypothetical protein LOC22889												0	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;8.82e-06)															---	---	---	---
PMF1	11243	broad.mit.edu	37	1	156199368	156199368	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156199368delT	uc001fnq.2	+						PMF1_uc009wru.1_Intron|PMF1_uc001fnr.2_Intron|BGLAP_uc001fns.1_Intron	NM_007221	NP_009152			polyamine-modulated factor 1						cell division|chromosome segregation|mitotic prometaphase|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytosol|MIS12/MIND type complex|transcription factor complex	leucine zipper domain binding|transcription coactivator activity				0	Hepatocellular(266;0.158)																	---	---	---	---
C1orf66	51093	broad.mit.edu	37	1	156702951	156702951	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156702951delT	uc001fpu.2	+						C1orf66_uc001fpv.2_Intron	NM_015997	NP_057081			hypothetical protein LOC51093 isoform 1							integral to membrane	rRNA (adenine-N6,N6-)-dimethyltransferase activity				0	all_hematologic(923;0.088)|Hepatocellular(266;0.158)																	---	---	---	---
PEAR1	375033	broad.mit.edu	37	1	156861082	156861082	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156861082delT	uc001fqj.1	+							NM_001080471	NP_001073940			platelet endothelial aggregation receptor 1							integral to membrane				ovary(2)|central_nervous_system(1)	3	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)																	---	---	---	---
ETV3L	440695	broad.mit.edu	37	1	157071368	157071371	+	5'Flank	DEL	AAAA	-	-	rs11418237		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157071368_157071371delAAAA	uc001fqq.1	-							NM_001004341	NP_001004341			ets variant 3-like							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4	Hepatocellular(266;0.158)	Prostate(1639;0.184)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	157306530	157306530	+	IGR	DEL	T	-	-	rs5778026		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157306530delT								ETV3 (198147 upstream) : FCRL5 (176638 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	157324055	157324055	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157324055delG								ETV3 (215672 upstream) : FCRL5 (159113 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	157481494	157481494	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157481494delT								ETV3 (373111 upstream) : FCRL5 (1674 downstream)																																			---	---	---	---
FCRL5	83416	broad.mit.edu	37	1	157503260	157503260	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157503260delT	uc001fqu.2	-						FCRL5_uc009wsm.2_Intron|FCRL5_uc010phv.1_Intron|FCRL5_uc010phw.1_Intron|FCRL5_uc001fqv.1_3'UTR	NM_031281	NP_112571			Fc receptor-like 5							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)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	157924431	157924432	+	IGR	INS	-	T	T	rs10683551		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157924431_157924432insT								CD5L (112797 upstream) : KIRREL (38631 downstream)																																			---	---	---	---
KIRREL	55243	broad.mit.edu	37	1	157984028	157984029	+	Intron	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157984028_157984029delAG	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	158035752	158035752	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158035752delT	uc001frn.3	+						KIRREL_uc010pib.1_Intron	NM_018240	NP_060710			kin of IRRE like precursor							integral to membrane				ovary(1)	1	all_hematologic(112;0.0378)																	---	---	---	---
SPTA1	6708	broad.mit.edu	37	1	158613927	158613928	+	Intron	DEL	AA	-	-	rs77912388		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158613927_158613928delAA	uc001fst.1	-							NM_003126	NP_003117			spectrin, alpha, erythrocytic 1						actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	158835806	158835806	+	IGR	DEL	C	-	-	rs143059193		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158835806delC								MNDA (16536 upstream) : PYHIN1 (65536 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	158846173	158846173	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158846173delT								MNDA (26903 upstream) : PYHIN1 (55169 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	159197641	159197641	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159197641delA								DARC (21353 upstream) : FCER1A (61865 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	159437001	159437001	+	Intron	DEL	A	-	-	rs140511868		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159437001delA	uc001fts.3	-											Homo sapiens, clone IMAGE:3917623, mRNA.																														---	---	---	---
SLAMF1	6504	broad.mit.edu	37	1	160599094	160599095	+	Intron	DEL	TC	-	-	rs71662098		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160599094_160599095delTC	uc001fwl.3	-						SLAMF1_uc010pjk.1_Intron|SLAMF1_uc010pjl.1_Intron|SLAMF1_uc010pjm.1_Intron	NM_003037	NP_003028			signaling lymphocytic activation molecule family						interspecies interaction between organisms|lymphocyte activation|positive regulation of cell proliferation	integral to membrane	antigen binding|transmembrane receptor activity			ovary(1)|breast(1)	2	all_cancers(52;4.94e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	160866050	160866050	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160866050delT								ITLN1 (11090 upstream) : ITLN2 (48767 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	160960334	160960334	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160960334delA								ITLN2 (35745 upstream) : F11R (4668 downstream)																																			---	---	---	---
UAP1	6675	broad.mit.edu	37	1	162543060	162543060	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162543060delA	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)															---	---	---	---
HSD17B7	51478	broad.mit.edu	37	1	162782018	162782018	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162782018delT	uc001gci.2	+						HSD17B7_uc009wuv.2_Intron	NM_016371	NP_057455			hydroxysteroid (17-beta) dehydrogenase 7						cholesterol biosynthetic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane	3-keto sterol reductase activity|estradiol 17-beta-dehydrogenase activity			ovary(1)	1	all_hematologic(112;0.115)				NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	163925607	163925608	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163925607_163925608insT								NUF2 (600054 upstream) : PBX1 (603194 downstream)																																			---	---	---	---
PBX1	5087	broad.mit.edu	37	1	164539143	164539143	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164539143delA	uc001gct.2	+						PBX1_uc010pku.1_Intron|PBX1_uc010pkv.1_Intron|PBX1_uc001gcs.2_Intron	NM_002585	NP_002576			pre-B-cell leukemia homeobox 1						negative regulation of sequence-specific DNA binding transcription factor activity|sex differentiation|steroid biosynthetic process	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription factor binding		EWSR1/PBX1(3)	soft_tissue(3)|lung(1)|skin(1)	5								T	TCF3|EWSR1	pre B-ALL|myoepithelioma								---	---	---	---
PBX1	5087	broad.mit.edu	37	1	164690666	164690667	+	Intron	DEL	GT	-	-	rs112904192		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164690666_164690667delGT	uc001gct.2	+						PBX1_uc010pku.1_Intron|PBX1_uc010pkv.1_Intron|PBX1_uc001gcs.2_Intron|PBX1_uc010pkw.1_Intron	NM_002585	NP_002576			pre-B-cell leukemia homeobox 1						negative regulation of sequence-specific DNA binding transcription factor activity|sex differentiation|steroid biosynthetic process	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription factor binding		EWSR1/PBX1(3)	soft_tissue(3)|lung(1)|skin(1)	5								T	TCF3|EWSR1	pre B-ALL|myoepithelioma								---	---	---	---
PBX1	5087	broad.mit.edu	37	1	164719347	164719347	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164719347delA	uc001gct.2	+						PBX1_uc010pku.1_Intron|PBX1_uc010pkv.1_Intron|PBX1_uc001gcs.2_Intron|PBX1_uc010pkw.1_Intron	NM_002585	NP_002576			pre-B-cell leukemia homeobox 1						negative regulation of sequence-specific DNA binding transcription factor activity|sex differentiation|steroid biosynthetic process	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription factor binding		EWSR1/PBX1(3)	soft_tissue(3)|lung(1)|skin(1)	5								T	TCF3|EWSR1	pre B-ALL|myoepithelioma								---	---	---	---
Unknown	0	broad.mit.edu	37	1	165581419	165581419	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165581419delA								LOC400794 (30078 upstream) : MGST3 (19031 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	166014501	166014501	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166014501delG								UCK2 (137164 upstream) : FAM78B (14915 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	166232144	166232144	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166232144delA								FAM78B (95938 upstream) : FMO9P (341009 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	166315232	166315232	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166315232delT								FAM78B (179026 upstream) : FMO9P (257921 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	166804814	166804815	+	IGR	INS	-	CTT	CTT	rs143374707	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166804814_166804815insCTT								FMO9P (210343 upstream) : POGK (3909 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	166855095	166855095	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166855095delT								TADA1 (9441 upstream) : ILDR2 (32901 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	167104358	167104358	+	IGR	DEL	A	-	-	rs66466415		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167104358delA								DUSP27 (5956 upstream) : POU2F1 (85785 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	167139247	167139247	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167139247delA								DUSP27 (40845 upstream) : POU2F1 (50896 downstream)																																			---	---	---	---
POU2F1	5451	broad.mit.edu	37	1	167187811	167187812	+	5'Flank	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167187811_167187812delTT	uc001gec.2	+						POU2F1_uc010plg.1_5'Flank|POU2F1_uc001ged.2_5'Flank|POU2F1_uc001gee.2_5'Flank|POU2F1_uc010plh.1_5'Flank	NM_002697	NP_002688			POU class 2 homeobox 1						negative regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|skin(2)|breast(1)	5																		---	---	---	---
POU2F1	5451	broad.mit.edu	37	1	167283437	167283437	+	Intron	DEL	A	-	-	rs75932518		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167283437delA	uc001gec.2	+						POU2F1_uc010plg.1_Intron|POU2F1_uc001ged.2_Intron|POU2F1_uc001gee.2_Intron|POU2F1_uc010plh.1_Intron	NM_002697	NP_002688			POU class 2 homeobox 1						negative regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|skin(2)|breast(1)	5																		---	---	---	---
GPR161	23432	broad.mit.edu	37	1	168107067	168107067	+	5'Flank	DEL	A	-	-	rs34593318		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168107067delA	uc001gfc.2	-						GPR161_uc001gfb.2_5'Flank|GPR161_uc010pll.1_5'Flank|GPR161_uc010plm.1_5'Flank|GPR161_uc009wvo.2_5'Flank|GPR161_uc001gfd.2_5'Flank|GPR161_uc010pln.1_5'Flank	NM_153832	NP_722561			G protein-coupled receptor 161 isoform 2						multicellular organismal development	integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_hematologic(923;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	168410087	168410090	+	IGR	DEL	GAGA	-	-	rs28533623		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168410087_168410090delGAGA								MIR557 (65228 upstream) : XCL2 (99915 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	168414869	168414869	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168414869delC								MIR557 (70010 upstream) : XCL2 (95136 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	168617689	168617689	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168617689delA								XCL1 (66374 upstream) : DPT (47018 downstream)																																			---	---	---	---
C1orf114	57821	broad.mit.edu	37	1	169366387	169366387	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169366387delT	uc001gga.1	-						C1orf114_uc001gfz.1_Intron|C1orf114_uc009wvq.1_Intron	NM_021179	NP_067002			hypothetical protein LOC57821												0	all_hematologic(923;0.208)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	169471241	169471242	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169471241_169471242insA								SLC19A2 (16033 upstream) : F5 (9950 downstream)																																			---	---	---	---
SELL	6402	broad.mit.edu	37	1	169677466	169677466	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169677466delC	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)																	---	---	---	---
SELE	6401	broad.mit.edu	37	1	169699840	169699841	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169699840_169699841delTT	uc001ggm.3	-						C1orf112_uc001ggj.2_Intron	NM_000450	NP_000441			selectin E precursor						actin filament-based process|activation of phospholipase C activity|calcium-mediated signaling|heterophilic cell-cell adhesion|leukocyte migration involved in inflammatory response|leukocyte tethering or rolling|positive regulation of receptor internalization|regulation of inflammatory response|response to interleukin-1|response to lipopolysaccharide|response to tumor necrosis factor	caveola|coated pit|cortical cytoskeleton|extracellular space|integral to membrane|perinuclear region of cytoplasm	oligosaccharide binding|phospholipase binding|sialic acid binding|transmembrane receptor activity			ovary(3)|skin(2)	5	all_hematologic(923;0.208)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	170536414	170536414	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170536414delA								GORAB (13440 upstream) : PRRX1 (96899 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	171201840	171201841	+	IGR	DEL	TT	-	-	rs34468722		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171201840_171201841delTT								FMO2 (20018 upstream) : FMO1 (15792 downstream)																																			---	---	---	---
BAT2L2	23215	broad.mit.edu	37	1	171452363	171452363	+	5'Flank	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171452363delA	uc010pmg.1	+						BAT2L2_uc001ghq.1_5'Flank|BAT2L2_uc001ghr.1_5'Flank	NM_015172	NP_055987			HBxAg transactivated protein 2								protein C-terminus binding				0																		---	---	---	---
RC3H1	149041	broad.mit.edu	37	1	173916418	173916418	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173916418delA	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	174232849	174232849	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174232849delT	uc001gjx.2	+						RABGAP1L_uc009wwq.1_Intron|RABGAP1L_uc001gjw.2_Intron|RABGAP1L_uc001gjy.2_Intron	NM_014857	NP_055672			RAB GTPase activating protein 1-like isoform A						regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4																		---	---	---	---
RABGAP1L	9910	broad.mit.edu	37	1	174278025	174278025	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174278025delT	uc001gjx.2	+						RABGAP1L_uc009wwq.1_Intron|RABGAP1L_uc001gjw.2_Intron|RABGAP1L_uc001gjy.2_Intron|RABGAP1L_uc001gjz.2_Intron	NM_014857	NP_055672			RAB GTPase activating protein 1-like isoform A						regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4																		---	---	---	---
RABGAP1L	9910	broad.mit.edu	37	1	174759348	174759348	+	Intron	DEL	A	-	-	rs112964112		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174759348delA	uc001gjx.2	+						RABGAP1L_uc001gkb.3_Intron|RABGAP1L_uc001gkc.3_Intron|RABGAP1L_uc001gkd.3_Intron	NM_014857	NP_055672			RAB GTPase activating protein 1-like isoform A						regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4																		---	---	---	---
TNN	63923	broad.mit.edu	37	1	175046454	175046455	+	Intron	INS	-	A	A	rs140606928	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175046454_175046455insA	uc001gkl.1	+						TNN_uc010pmx.1_5'Flank	NM_022093	NP_071376			tenascin N precursor						cell growth|cell migration|signal transduction	extracellular space|proteinaceous extracellular matrix				large_intestine(5)|ovary(3)|central_nervous_system(1)	9		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	175854790	175854790	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175854790delC								TNR (142038 upstream) : RFWD2 (59177 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	175880378	175880378	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175880378delA								TNR (167626 upstream) : RFWD2 (33589 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	175891943	175891943	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175891943delT								TNR (179191 upstream) : RFWD2 (22024 downstream)																																			---	---	---	---
PAPPA2	60676	broad.mit.edu	37	1	176770227	176770228	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176770227_176770228delAC	uc001gkz.2	+						PAPPA2_uc009www.2_Intron	NM_020318	NP_064714			pappalysin 2 isoform 1						cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16																		---	---	---	---
ASTN1	460	broad.mit.edu	37	1	177112038	177112042	+	Intron	DEL	AAGGG	-	-	rs59942849		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177112038_177112042delAAGGG	uc001glc.2	-						ASTN1_uc001glb.1_Intron|ASTN1_uc001gld.1_Intron|ASTN1_uc009wwx.1_Intron	NM_004319	NP_004310			astrotactin isoform 1						cell migration|neuron cell-cell adhesion	integral to membrane				ovary(6)|skin(5)|central_nervous_system(2)|large_intestine(1)|lung(1)	15																		---	---	---	---
FAM5B	57795	broad.mit.edu	37	1	177151791	177151792	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177151791_177151792insT	uc001glf.2	+							NM_021165	NP_066988			family with sequence similarity 5, member B							extracellular region				skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	177821755	177821755	+	IGR	DEL	A	-	-	rs68043095		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177821755delA								FAM5B (570198 upstream) : SEC16B (75734 downstream)																																			---	---	---	---
SEC16B	89866	broad.mit.edu	37	1	177973742	177973742	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177973742delA	uc001glj.1	-						SEC16B_uc001glk.1_Intron	NM_033127	NP_149118			leucine zipper transcription regulator 2						protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane				ovary(3)|central_nervous_system(1)	4																		---	---	---	---
SOAT1	6646	broad.mit.edu	37	1	179309407	179309407	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179309407delA	uc001gml.2	+						SOAT1_uc010pni.1_Intron|SOAT1_uc001gmm.2_Intron|SOAT1_uc010pnj.1_Intron|SOAT1_uc010pnk.1_Intron	NM_003101	NP_003092			sterol O-acyltransferase 1						cholesterol efflux|cholesterol esterification|cholesterol homeostasis|cholesterol metabolic process|cholesterol storage|macrophage derived foam cell differentiation|positive regulation of amyloid precursor protein biosynthetic process|very-low-density lipoprotein particle assembly	endoplasmic reticulum membrane|integral to membrane|microsome	cholesterol binding|cholesterol O-acyltransferase activity|fatty-acyl-CoA binding			central_nervous_system(1)|skin(1)	2					Ezetimibe(DB00973)|Hesperetin(DB01094)													---	---	---	---
C1orf125	126859	broad.mit.edu	37	1	179362616	179362616	+	Intron	DEL	T	-	-	rs143006628		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179362616delT	uc001gmo.2	+						C1orf125_uc009wxg.2_Intron|C1orf125_uc001gmn.1_Intron|C1orf125_uc010pnl.1_Intron|C1orf125_uc001gmp.2_Intron	NM_144696	NP_653297			hypothetical protein LOC126859 isoform 1												0																		---	---	---	---
QSOX1	5768	broad.mit.edu	37	1	180140374	180140374	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180140374delG	uc001gnz.2	+						QSOX1_uc001gny.2_Intron|QSOX1_uc001goa.2_Intron	NM_002826	NP_002817			quiescin Q6 sulfhydryl oxidase 1 isoform a						cell redox homeostasis|protein thiol-disulfide exchange	extracellular space|integral to Golgi membrane	flavin-linked sulfhydryl oxidase activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
XPR1	9213	broad.mit.edu	37	1	180615532	180615532	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180615532delT	uc001goi.2	+						XPR1_uc009wxm.2_Intron|XPR1_uc009wxn.2_Intron	NM_004736	NP_004727			xenotropic and polytropic retrovirus receptor							integral to plasma membrane	G-protein coupled receptor activity				0																		---	---	---	---
XPR1	9213	broad.mit.edu	37	1	180649174	180649174	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180649174delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	181028303	181028303	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181028303delT								MR1 (3670 upstream) : IER5 (29335 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	182064600	182064600	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182064600delG								ZNF648 (33753 upstream) : GLUL (287069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	183151735	183151737	+	IGR	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183151735_183151737delTTT								LAMC1 (37009 upstream) : LAMC2 (3437 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	184246219	184246220	+	IGR	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184246219_184246220delCT								TSEN15 (202878 upstream) : C1orf21 (109930 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	184270237	184270237	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184270237delG								TSEN15 (226896 upstream) : C1orf21 (85913 downstream)																																			---	---	---	---
C1orf21	81563	broad.mit.edu	37	1	184446788	184446788	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184446788delT	uc001gqv.1	+							NM_030806	NP_110433			chromosome 1 open reading frame 21												0		Breast(1374;0.00262)		Colorectal(1306;4.8e-08)|KIRC - Kidney renal clear cell carcinoma(1967;0.00314)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	184969737	184969737	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184969737delT								FAM129A (26055 upstream) : RNF2 (44814 downstream)																																			---	---	---	---
RNF2	6045	broad.mit.edu	37	1	185062937	185062937	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185062937delT	uc001grc.1	+						RNF2_uc001grd.1_Intron|RNF2_uc001gre.1_Intron	NM_007212	NP_009143			ring finger protein 2						histone H2A monoubiquitination|transcription, DNA-dependent	MLL1 complex|PcG protein complex|ubiquitin ligase complex	RING-like zinc finger domain binding|zinc ion binding			breast(1)	1		Breast(1374;0.000496)		Colorectal(1306;6.9e-08)|KIRC - Kidney renal clear cell carcinoma(1967;8.12e-06)														---	---	---	---
C1orf26	54823	broad.mit.edu	37	1	185245916	185245916	+	Intron	DEL	T	-	-	rs143251562		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	185414884	185414884	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185414884delT								IVNS1ABP (128423 upstream) : HMCN1 (288799 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	185656604	185656611	+	IGR	DEL	CTCCCTCC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185656604_185656611delCTCCCTCC								IVNS1ABP (370143 upstream) : HMCN1 (47072 downstream)																																			---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	186077432	186077432	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186077432delA	uc001grq.1	+							NM_031935	NP_114141			hemicentin 1 precursor						response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
TPR	7175	broad.mit.edu	37	1	186296921	186296921	+	Intron	DEL	T	-	-	rs71745453		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186296921delT	uc001grv.2	-							NM_003292	NP_003283			nuclear pore complex-associated protein TPR						carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm	ATP binding|protein binding|serine-tRNA ligase activity			ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1)	7		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)				T	NTRK1	papillary thyroid								---	---	---	---
C1orf27	54953	broad.mit.edu	37	1	186357523	186357523	+	Intron	DEL	T	-	-	rs1290390	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186357523delT	uc001grw.2	+						C1orf27_uc010poq.1_Intron|C1orf27_uc010por.1_Intron	NM_017847	NP_060317			odorant response abnormal 4 isoform 1							integral to membrane	oxidoreductase activity|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	187009627	187009628	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187009627_187009628delTT								PLA2G4A (51522 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	187962681	187962682	+	IGR	DEL	AA	-	-	rs113590189		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187962681_187962682delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	187980924	187980924	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187980924delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	188416136	188416139	+	IGR	DEL	TTCC	-	-	rs112749943		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:188416136_188416139delTTCC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	189217044	189217044	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189217044delT								None (None upstream) : FAM5C (849753 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	189479447	189479447	+	IGR	DEL	C	-	-	rs67024578		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189479447delC								None (None upstream) : FAM5C (587350 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	189650676	189650676	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189650676delA								None (None upstream) : FAM5C (416121 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	191083473	191083473	+	IGR	DEL	A	-	-	rs34535993		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:191083473delA								FAM5C (636714 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	191915202	191915202	+	IGR	DEL	T	-	-	rs6697186	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:191915202delT								None (None upstream) : RGS18 (212390 downstream)																																			---	---	---	---
RGS18	64407	broad.mit.edu	37	1	192128012	192128012	+	Intron	DEL	A	-	-	rs28417375		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192128012delA	uc001gsg.2	+							NM_130782	NP_570138			regulator of G-protein signalling 18						negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	192243305	192243306	+	IGR	INS	-	AA	AA	rs150736558	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192243305_192243306insAA								RGS18 (88362 upstream) : RGS21 (42816 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	193556148	193556148	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193556148delT								CDC73 (332208 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	193642833	193642833	+	IGR	DEL	T	-	-	rs75557855		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193642833delT								CDC73 (418893 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	194029871	194029872	+	IGR	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:194029871_194029872delAG								CDC73 (805931 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	195466582	195466582	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:195466582delT								None (None upstream) : KCNT2 (728331 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	195537091	195537091	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:195537091delA								None (None upstream) : KCNT2 (657822 downstream)																																			---	---	---	---
KCNT2	343450	broad.mit.edu	37	1	196503232	196503233	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196503232_196503233insA	uc001gtd.1	-						KCNT2_uc001gte.1_Intron|KCNT2_uc001gtf.1_Intron|KCNT2_uc001gtg.1_Intron|KCNT2_uc009wyu.2_Intron|KCNT2_uc009wyv.1_Intron	NM_198503	NP_940905			potassium channel, subfamily T, member 2							voltage-gated potassium channel complex	ATP binding|calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(5)|breast(1)|skin(1)	7																		---	---	---	---
CFH	3075	broad.mit.edu	37	1	196683153	196683153	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196683153delA	uc001gtj.3	+							NM_000186	NP_000177			complement factor H isoform a precursor						complement activation, alternative pathway	extracellular space				skin(4)|ovary(1)|breast(1)	6																		---	---	---	---
CRB1	23418	broad.mit.edu	37	1	197427490	197427490	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197427490delT	uc001gtz.2	+						CRB1_uc010poz.1_Intron|CRB1_uc010ppa.1_Intron|CRB1_uc009wza.2_Intron|CRB1_uc010ppb.1_Intron|CRB1_uc010ppd.1_Intron	NM_201253	NP_957705			crumbs homolog 1 precursor						cell-cell signaling|establishment or maintenance of cell polarity	apical plasma membrane|extracellular region|integral to membrane	calcium ion binding|protein binding			ovary(5)|skin(3)|large_intestine(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	198827134	198827134	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198827134delA								PTPRC (100589 upstream) : MIR181B1 (868 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	199457359	199457359	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199457359delT								MIR181A1 (629077 upstream) : NR5A2 (539411 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	199696185	199696185	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199696185delA								MIR181A1 (867903 upstream) : NR5A2 (300585 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	199948618	199948618	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199948618delT								None (None upstream) : NR5A2 (48152 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	200317846	200317846	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200317846delA	uc001gvd.1	-											Homo sapiens chromosome 1 open reading frame 98, mRNA (cDNA clone IMAGE:5197767).																														---	---	---	---
KIF14	9928	broad.mit.edu	37	1	200524466	200524466	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200524466delA	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	200734746	200734746	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200734746delA	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																		---	---	---	---
TMEM9	252839	broad.mit.edu	37	1	201125662	201125662	+	5'Flank	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201125662delC	uc001gvw.2	-						TMEM9_uc001gvx.2_5'Flank|TMEM9_uc001gvy.2_5'Flank|TMEM9_uc010ppo.1_5'Flank|TMEM9_uc001gvz.2_5'Flank|TMEM9_uc001gwa.2_Intron|TMEM9_uc010ppp.1_5'Flank	NM_016456	NP_057540			transmembrane protein 9 precursor						transport	integral to membrane|late endosome membrane|lysosomal membrane					0		Breast(1374;0.000301)																---	---	---	---
IPO9	55705	broad.mit.edu	37	1	201821197	201821197	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201821197delT	uc001gwz.2	+							NM_018085	NP_060555			importin 9						protein import into nucleus	cytoplasm|nucleus	histone binding|protein transporter activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	202078438	202078438	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202078438delC								ELF3 (92132 upstream) : GPR37L1 (13591 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	202780874	202780878	+	IGR	DEL	CAATT	-	-	rs72442869	byFrequency	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202780874_202780878delCAATT								KDM5B (3325 upstream) : LOC148709 (50004 downstream)																																			---	---	---	---
LOC148709	148709	broad.mit.edu	37	1	202833891	202833892	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202833891_202833892insA	uc001gyk.1	+							NR_002929				Homo sapiens cDNA FLJ31247 fis, clone KIDNE2005296, weakly similar to ACTIN, CYTOPLASMIC 1.												0																		---	---	---	---
MYOG	4656	broad.mit.edu	37	1	203052857	203052857	+	3'UTR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203052857delC	uc001gzd.2	-	3						NM_002479	NP_002470			myogenin						muscle cell fate commitment|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter	transcription factor complex	E-box binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity			skin(2)	2																		---	---	---	---
ATP2B4	493	broad.mit.edu	37	1	203712714	203712715	+	3'UTR	DEL	AT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203712714_203712715delAT	uc001gzw.2	+	21					ATP2B4_uc001gzv.2_3'UTR|ATP2B4_uc001gzx.2_3'UTR|ATP2B4_uc009xar.2_3'UTR	NM_001684	NP_001675			plasma membrane calcium ATPase 4 isoform 4b						ATP biosynthetic process|platelet activation	integral to plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding|protein binding			ovary(2)|skin(1)	3	all_cancers(21;0.071)|all_epithelial(62;0.228)		BRCA - Breast invasive adenocarcinoma(75;0.109)															---	---	---	---
ZC3H11A	9877	broad.mit.edu	37	1	203816133	203816133	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203816133delA	uc001hac.2	+						ZC3H11A_uc001had.2_Intron|ZC3H11A_uc001hae.2_Intron|ZC3H11A_uc001haf.2_Intron|ZC3H11A_uc010pqm.1_Intron|ZC3H11A_uc001hag.1_Intron	NM_014827	NP_055642			zinc finger CCCH-type containing 11A								nucleic acid binding|protein binding|zinc ion binding			lung(1)|central_nervous_system(1)	2	all_cancers(21;0.0904)|all_epithelial(62;0.234)		BRCA - Breast invasive adenocarcinoma(75;0.109)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	203886458	203886460	+	IGR	DEL	AAC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203886458_203886460delAAC								SNRPE (46180 upstream) : C1orf157 (115115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	203918126	203918127	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203918126_203918127delAA								SNRPE (77848 upstream) : C1orf157 (83448 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	204018509	204018509	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204018509delT								C1orf157 (8117 upstream) : SOX13 (23737 downstream)																																			---	---	---	---
PIK3C2B	5287	broad.mit.edu	37	1	204451892	204451892	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204451892delA	uc001haw.2	-						PIK3C2B_uc010pqv.1_Intron|PIK3C2B_uc001hax.1_Intron|PIK3C2B_uc009xbd.1_Intron	NM_002646	NP_002637			phosphoinositide-3-kinase, class 2 beta						cell communication|phosphatidylinositol-mediated signaling	endoplasmic reticulum|microsome|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity|protein binding			lung(2)|breast(2)|stomach(1)|prostate(1)|central_nervous_system(1)	7	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)															---	---	---	---
NFASC	23114	broad.mit.edu	37	1	204964419	204964420	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204964419_204964420insT	uc001hbj.2	+						NFASC_uc010pra.1_Intron|NFASC_uc001hbi.2_Intron|NFASC_uc010prb.1_Intron|NFASC_uc010prc.1_Intron|NFASC_uc001hbl.1_Intron|NFASC_uc001hbm.1_Intron|NFASC_uc001hbn.1_Intron|NFASC_uc009xbh.1_5'Flank	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	205431018	205431018	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205431018delA	uc001hco.1	+											Homo sapiens cDNA FLJ38314 fis, clone FCBBF3022765.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	205854631	205854631	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205854631delT	uc001hdk.1	+											Homo sapiens cDNA FLJ31184 fis, clone KIDNE2000328.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	207018877	207018878	+	IGR	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207018877_207018878delGT								IL19 (2553 upstream) : IL20 (19821 downstream)																																			---	---	---	---
FCAMR	83953	broad.mit.edu	37	1	207132821	207132822	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207132821_207132822delAA	uc001hfa.3	-						FCAMR_uc001hfb.2_Intron|FCAMR_uc009xca.1_Intron|FCAMR_uc001hfc.2_Intron	NM_001122980	NP_001116452			Fc receptor, IgA, IgM, high affinity isoform 2							integral to membrane|plasma membrane	receptor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	207273399	207273414	+	IGR	DEL	ATGTGTGTGTGTGTGT	-	-	rs57088528		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207273399_207273414delATGTGTGTGTGTGTGT								C4BPB (64 upstream) : C4BPA (4097 downstream)																																			---	---	---	---
CD46	4179	broad.mit.edu	37	1	207947554	207947554	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	209480696	209480696	+	IGR	DEL	A	-	-	rs140335519		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209480696delA								None (None upstream) : LOC642587 (121472 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	209498049	209498049	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209498049delT								None (None upstream) : LOC642587 (104119 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	209582688	209582688	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209582688delT								None (None upstream) : LOC642587 (19480 downstream)																																			---	---	---	---
HSD11B1	3290	broad.mit.edu	37	1	209888758	209888758	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209888758delA	uc001hhj.2	+						HSD11B1_uc001hhk.2_Intron	NM_181755	NP_861420			11-beta-hydroxysteroid dehydrogenase 1						glucocorticoid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	11-beta-hydroxysteroid dehydrogenase (NADP+) activity|11-beta-hydroxysteroid dehydrogenase|binding			breast(1)	1				OV - Ovarian serous cystadenocarcinoma(81;1.04e-55)|Epithelial(68;1.57e-52)|all cancers(67;1.83e-46)|Colorectal(1306;0.115)	NADH(DB00157)													---	---	---	---
HSD11B1	3290	broad.mit.edu	37	1	209893463	209893463	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209893463delT	uc001hhj.2	+						HSD11B1_uc001hhk.2_Intron	NM_181755	NP_861420			11-beta-hydroxysteroid dehydrogenase 1						glucocorticoid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	11-beta-hydroxysteroid dehydrogenase (NADP+) activity|11-beta-hydroxysteroid dehydrogenase|binding			breast(1)	1				OV - Ovarian serous cystadenocarcinoma(81;1.04e-55)|Epithelial(68;1.57e-52)|all cancers(67;1.83e-46)|Colorectal(1306;0.115)	NADH(DB00157)													---	---	---	---
TRAF3IP3	80342	broad.mit.edu	37	1	209935223	209935223	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209935223delA	uc001hho.2	+						TRAF3IP3_uc001hhl.2_Intron|TRAF3IP3_uc001hhm.1_Intron|TRAF3IP3_uc001hhn.2_Intron|TRAF3IP3_uc009xcr.2_Intron	NM_025228	NP_079504			TRAF3-interacting JNK-activating modulator							integral to membrane	protein binding			large_intestine(1)|ovary(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.045)														---	---	---	---
SYT14	255928	broad.mit.edu	37	1	210293690	210293690	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210293690delT	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	210429962	210429962	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210429962delA								SERTAD4 (13524 upstream) : HHAT (71644 downstream)																																			---	---	---	---
KCNH1	3756	broad.mit.edu	37	1	211281745	211281746	+	Intron	INS	-	GA	GA	rs68134280		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211281745_211281746insGA	uc001hib.2	-						KCNH1_uc001hic.2_Intron	NM_172362	NP_758872			potassium voltage-gated channel, subfamily H,						myoblast fusion|regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	calmodulin binding|delayed rectifier potassium channel activity|two-component sensor activity			ovary(4)|central_nervous_system(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)														---	---	---	---
INTS7	25896	broad.mit.edu	37	1	212180338	212180339	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212180338_212180339delTT	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)														---	---	---	---
TATDN3	128387	broad.mit.edu	37	1	212977997	212977997	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212977997delT	uc001hjo.2	+						TATDN3_uc010ptj.1_Intron|TATDN3_uc010ptk.1_Intron|TATDN3_uc001hjp.2_Intron|TATDN3_uc010ptl.1_Intron|TATDN3_uc010ptm.1_Intron	NM_001042552	NP_001036017			TatD DNase domain containing 3 isoform 1							nucleus	endodeoxyribonuclease activity, producing 5'-phosphomonoesters|metal ion binding				0				OV - Ovarian serous cystadenocarcinoma(81;0.00699)|all cancers(67;0.0118)|GBM - Glioblastoma multiforme(131;0.0801)|Epithelial(68;0.104)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	214853205	214853206	+	IGR	INS	-	CT	CT			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214853205_214853206insCT								CENPF (15293 upstream) : KCNK2 (325679 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	214908957	214908958	+	IGR	INS	-	TG	TG	rs72065590		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214908957_214908958insTG								CENPF (71045 upstream) : KCNK2 (269927 downstream)																																			---	---	---	---
KCTD3	51133	broad.mit.edu	37	1	215749407	215749407	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215749407delT	uc001hks.2	+						KCTD3_uc001hkt.2_Intron|KCTD3_uc010pub.1_Intron|KCTD3_uc009xdn.2_5'Flank	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)														---	---	---	---
KCTD3	51133	broad.mit.edu	37	1	215773690	215773690	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215773690delT	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	215914591	215914592	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215914591_215914592insA	uc001hku.1	-							NM_206933	NP_996816			usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)											HNSCC(13;0.011)			---	---	---	---
ESRRG	2104	broad.mit.edu	37	1	216876647	216876647	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216876647delA	uc001hkw.1	-						ESRRG_uc001hky.1_Intron|ESRRG_uc009xdp.1_Intron|ESRRG_uc001hkz.1_Intron|ESRRG_uc010puc.1_Intron|ESRRG_uc001hla.1_Intron|ESRRG_uc001hlb.1_Intron|ESRRG_uc010pud.1_Intron|ESRRG_uc001hlc.1_Intron|ESRRG_uc001hld.1_Intron|ESRRG_uc001hkx.1_Intron|ESRRG_uc009xdo.1_Intron|ESRRG_uc001hle.1_Intron	NM_001438	NP_001429			estrogen-related receptor gamma isoform 1						positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	AF-2 domain binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|kidney(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)													---	---	---	---
ESRRG	2104	broad.mit.edu	37	1	216934436	216934436	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216934436delA	uc001hky.1	-						ESRRG_uc009xdp.1_Intron|ESRRG_uc001hkz.1_Intron|ESRRG_uc010puc.1_Intron|ESRRG_uc001hla.1_Intron|ESRRG_uc001hlb.1_Intron|ESRRG_uc010pud.1_Intron|ESRRG_uc001hlc.1_Intron|ESRRG_uc001hld.1_Intron	NM_206595	NP_996318			estrogen-related receptor gamma isoform 2						positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	AF-2 domain binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|kidney(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)													---	---	---	---
GPATCH2	55105	broad.mit.edu	37	1	217711391	217711391	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217711391delA	uc001hlf.1	-							NM_018040	NP_060510			G patch domain containing 2							intracellular	nucleic acid binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0397)|all cancers(67;0.0744)|GBM - Glioblastoma multiforme(131;0.0872)														---	---	---	---
SPATA17	128153	broad.mit.edu	37	1	217977366	217977367	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217977366_217977367delAA	uc001hlh.1	+						SPATA17_uc001hli.2_Intron	NM_138796	NP_620151			spermatogenesis associated 17							cytoplasm	calmodulin binding			pancreas(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0516)|all cancers(67;0.0891)|GBM - Glioblastoma multiforme(131;0.117)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	218664283	218664283	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218664283delT								TGFB2 (46324 upstream) : LYPLAL1 (682909 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	219188258	219188258	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219188258delT								TGFB2 (570299 upstream) : LYPLAL1 (158934 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	219283442	219283442	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219283442delG	uc001hlp.2	-											Homo sapiens cDNA clone IMAGE:6189076.																														---	---	---	---
LYPLAL1	127018	broad.mit.edu	37	1	219365971	219365971	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219365971delT	uc001hlq.3	+						LYPLAL1_uc001hlr.3_Intron|LYPLAL1_uc001hls.3_Intron|LYPLAL1_uc001hlt.3_Intron|LYPLAL1_uc009xds.2_Intron	NM_138794	NP_620149			lysophospholipase-like 1							cytoplasm	lysophospholipase activity				0				GBM - Glioblastoma multiforme(131;0.055)|all cancers(67;0.105)|OV - Ovarian serous cystadenocarcinoma(81;0.116)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	219570801	219570801	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219570801delT								LYPLAL1 (184595 upstream) : SLC30A10 (287968 downstream)																																			---	---	---	---
RAB3GAP2	25782	broad.mit.edu	37	1	220324483	220324483	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220324483delA	uc010puk.1	-	35					RAB3GAP2_uc001hmf.2_RNA|RAB3GAP2_uc001hmg.2_3'UTR|RAB3GAP2_uc001hmh.2_3'UTR	NM_012414	NP_036546			rab3 GTPase-activating protein, non-catalytic						intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(131;0.0443)														---	---	---	---
RAB3GAP2	25782	broad.mit.edu	37	1	220428057	220428057	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220428057delT	uc010puk.1	-						RAB3GAP2_uc001hmf.2_Intron|RAB3GAP2_uc001hmg.2_Intron|RAB3GAP2_uc010pum.1_Intron	NM_012414	NP_036546			rab3 GTPase-activating protein, non-catalytic						intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(131;0.0443)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	220516663	220516664	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220516663_220516664delTT								RAB3GAP2 (70820 upstream) : MARK1 (184904 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	221251382	221251382	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221251382delT								HLX (192984 upstream) : LOC400804 (251888 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	221307068	221307068	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221307068delA								HLX (248670 upstream) : LOC400804 (196202 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	221841416	221841417	+	IGR	INS	-	C	C	rs140669181	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221841416_221841417insC								LOC400804 (331778 upstream) : DUSP10 (33349 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	222198066	222198067	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222198066_222198067delTG								DUSP10 (282605 upstream) : HHIPL2 (497535 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	223282470	223282471	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223282470_223282471delTG								DISP1 (103135 upstream) : TLR5 (1113 downstream)																																			---	---	---	---
TLR5	7100	broad.mit.edu	37	1	223283695	223283695	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223283695delA	uc001hnv.1	-	4					TLR5_uc001hnw.1_3'UTR	NM_003268	NP_003259			toll-like receptor 5 precursor						cellular response to mechanical stimulus|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of interleukin-8 production|positive regulation of toll-like receptor signaling pathway	integral to membrane|plasma membrane	interleukin-1 receptor binding|transmembrane receptor activity			ovary(2)|lung(1)|skin(1)	4				GBM - Glioblastoma multiforme(131;0.0851)														---	---	---	---
FBXO28	23219	broad.mit.edu	37	1	224325991	224325991	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224325991delT	uc001hoh.2	+						FBXO28_uc009xef.2_Intron|FBXO28_uc010pvc.1_Intron	NM_015176	NP_055991			F-box protein 28 isoform a											ovary(2)|kidney(2)|lung(1)	5	Breast(184;0.206)			GBM - Glioblastoma multiforme(131;0.0363)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	224704588	224704589	+	Intron	INS	-	TT	TT			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224704588_224704589insTT	uc001hor.1	+											full-length cDNA clone CS0DC026YN07 of Neuroblastoma Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	225664335	225664336	+	IGR	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225664335_225664336delGT								LBR (47816 upstream) : ENAH (10198 downstream)																																			---	---	---	---
SRP9	6726	broad.mit.edu	37	1	225963580	225963581	+	5'Flank	INS	-	AG	AG	rs146918694	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225963580_225963581insAG	uc001hpg.2	+						SRP9_uc001hpf.3_5'Flank|SRP9_uc001hph.2_5'Flank|SRP9_uc001hpi.3_5'Flank|SRP9_uc001hpj.1_5'Flank	NM_003133	NP_003124			signal recognition particle 9kDa isoform 2						negative regulation of translational elongation|SRP-dependent cotranslational protein targeting to membrane	cytosol|signal recognition particle receptor complex|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding|signal recognition particle binding				0																		---	---	---	---
LIN9	286826	broad.mit.edu	37	1	226433130	226433130	+	Intron	DEL	C	-	-	rs67587255		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226433130delC	uc001hqa.2	-						LIN9_uc001hqb.2_Intron|LIN9_uc001hqc.2_Intron|LIN9_uc009xel.1_Intron	NM_173083	NP_775106			lin-9 homolog						cell cycle|DNA replication	nucleoplasm					0	Breast(184;0.158)			GBM - Glioblastoma multiforme(131;0.131)														---	---	---	---
LIN9	286826	broad.mit.edu	37	1	226438518	226438518	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226438518delA	uc001hqa.2	-						LIN9_uc001hqb.2_Intron|LIN9_uc001hqc.2_Intron|LIN9_uc009xel.1_Intron	NM_173083	NP_775106			lin-9 homolog						cell cycle|DNA replication	nucleoplasm					0	Breast(184;0.158)			GBM - Glioblastoma multiforme(131;0.131)														---	---	---	---
ZNF678	339500	broad.mit.edu	37	1	227755958	227755958	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227755958delA	uc001hqw.1	+						ZNF678_uc009xet.1_Intron|ZNF678_uc009xeu.1_Intron	NM_178549	NP_848644			zinc finger protein 678						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding			pancreas(1)	1		Prostate(94;0.0885)																---	---	---	---
ZNF678	339500	broad.mit.edu	37	1	227875052	227875052	+	Intron	DEL	A	-	-	rs60918477	byFrequency;by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227875052delA	uc009xeu.1	+											Homo sapiens cDNA: FLJ22822 fis, clone KAIA3968.						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding			pancreas(1)	1		Prostate(94;0.0885)																---	---	---	---
GUK1	2987	broad.mit.edu	37	1	228329606	228329606	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228329606delG	uc001hsh.2	+						GUK1_uc001hsi.2_Intron|GUK1_uc001hsj.2_Intron|GUK1_uc010pvv.1_5'Flank	NM_000858	NP_000849			guanylate kinase 1 isoform b						nucleobase, nucleoside and nucleotide interconversion|purine nucleotide metabolic process	cytosol	ATP binding|guanylate kinase activity				0		Prostate(94;0.0405)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	228575560	228575562	+	IGR	DEL	TTT	-	-	rs111523545		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228575560_228575562delTTT								OBSCN (8985 upstream) : TRIM11 (5817 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	228983721	228983721	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228983721delT								RHOU (101312 upstream) : RAB4A (423158 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	229072568	229072568	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229072568delA								RHOU (190159 upstream) : RAB4A (334311 downstream)																																			---	---	---	---
NUP133	55746	broad.mit.edu	37	1	229631436	229631436	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229631436delA	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	229894425	229894425	+	IGR	DEL	G	-	-	rs68101226		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229894425delG								URB2 (98479 upstream) : GALNT2 (299111 downstream)																																			---	---	---	---
PGBD5	79605	broad.mit.edu	37	1	230467405	230467405	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230467405delT	uc010pwb.1	-						PGBD5_uc001htv.2_Intron	NM_024554	NP_078830			piggyBac transposable element derived 5							integral to membrane				ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(184;0.0397)	Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;0.201)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	230545586	230545586	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230545586delA								PGBD5 (32219 upstream) : COG2 (232616 downstream)																																			---	---	---	---
EGLN1	54583	broad.mit.edu	37	1	231524392	231524393	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231524392_231524393insT	uc001huv.2	-						EGLN1_uc001huu.3_Intron	NM_022051	NP_071334			egl nine homolog 1						negative regulation of sequence-specific DNA binding transcription factor activity|oxygen homeostasis|response to hypoxia	cytosol	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptidyl-proline dioxygenase activity|protein binding|zinc ion binding				0		Prostate(94;0.194)|Acute lymphoblastic leukemia(190;0.244)			Vitamin C(DB00126)													---	---	---	---
TSNAX-DISC1	100303453	broad.mit.edu	37	1	231686950	231686950	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231686950delA	uc010pwg.1	+						TSNAX-DISC1_uc010pwe.1_Intron|TSNAX-DISC1_uc010pwf.1_Intron|TSNAX-DISC1_uc010pwh.1_Intron|TSNAX-DISC1_uc010pwi.1_Intron|TSNAX-DISC1_uc010pwj.1_Intron|TSNAX-DISC1_uc010pwk.1_Intron|TSNAX-DISC1_uc010pwl.1_Intron|TSNAX_uc001huw.2_Intron	NM_001012959	NP_001012977			disrupted in schizophrenia 1 isoform S												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	232525359	232525359	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232525359delA								DISC1 (348343 upstream) : SIPA1L2 (8355 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	232845206	232845206	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232845206delG								SIPA1L2 (193963 upstream) : KIAA1383 (95432 downstream)																																			---	---	---	---
PCNXL2	80003	broad.mit.edu	37	1	233266055	233266055	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233266055delC	uc001hvl.2	-						PCNXL2_uc001hvm.1_Intron|PCNXL2_uc009xfu.2_Intron|PCNXL2_uc001hvp.1_Intron|PCNXL2_uc009xfv.1_Intron	NM_014801	NP_055616			pecanex-like 2							integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	233644072	233644072	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233644072delT								KIAA1804 (123179 upstream) : KCNK1 (105678 downstream)																																			---	---	---	---
SLC35F3	148641	broad.mit.edu	37	1	234086594	234086594	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234086594delT	uc001hvy.1	+							NM_173508	NP_775779			solute carrier family 35, member F3						transport	integral to membrane				ovary(2)	2	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)															---	---	---	---
SLC35F3	148641	broad.mit.edu	37	1	234145492	234145492	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234145492delA	uc001hvy.1	+							NM_173508	NP_775779			solute carrier family 35, member F3						transport	integral to membrane				ovary(2)	2	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)															---	---	---	---
SLC35F3	148641	broad.mit.edu	37	1	234251571	234251575	+	Intron	DEL	ATCTC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234251571_234251575delATCTC	uc001hvy.1	+							NM_173508	NP_775779			solute carrier family 35, member F3						transport	integral to membrane				ovary(2)	2	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)															---	---	---	---
SLC35F3	148641	broad.mit.edu	37	1	234365007	234365008	+	Intron	INS	-	T	T	rs148003821	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234365007_234365008insT	uc001hwa.1	+						SLC35F3_uc001hvy.1_Intron	NM_173508	NP_775779			solute carrier family 35, member F3						transport	integral to membrane				ovary(2)	2	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)															---	---	---	---
SLC35F3	148641	broad.mit.edu	37	1	234416828	234416828	+	Intron	DEL	C	-	-	rs111906874		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234416828delC	uc001hwa.1	+						SLC35F3_uc001hvy.1_Intron	NM_173508	NP_775779			solute carrier family 35, member F3						transport	integral to membrane				ovary(2)	2	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)															---	---	---	---
IRF2BP2	359948	broad.mit.edu	37	1	234742205	234742205	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234742205delA	uc001hwg.2	-	2					IRF2BP2_uc009xfw.2_3'UTR|IRF2BP2_uc001hwf.2_3'UTR	NM_182972	NP_892017			interferon regulatory factor 2 binding protein 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0	Ovarian(103;0.0303)	all_cancers(173;0.0236)|Prostate(94;0.0115)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)|Epithelial(3;6.2e-05)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	234964157	234964157	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234964157delT								IRF2BP2 (218886 upstream) : TOMM20 (308503 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	235025071	235025073	+	IGR	DEL	AAA	-	-	rs35994610		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235025071_235025073delAAA								IRF2BP2 (279800 upstream) : TOMM20 (247587 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	235051636	235051636	+	IGR	DEL	A	-	-	rs11314386		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235051636delA								IRF2BP2 (306365 upstream) : TOMM20 (221024 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	235128474	235128474	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235128474delT								IRF2BP2 (383203 upstream) : TOMM20 (144186 downstream)																																			---	---	---	---
RBM34	23029	broad.mit.edu	37	1	235298365	235298365	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235298365delT	uc001hwn.2	-						RBM34_uc001hwo.2_Intron|ARID4B_uc001hwp.2_Intron	NM_015014	NP_055829			RNA binding motif protein 34 isoform 1							nucleolus	nucleotide binding|RNA binding			central_nervous_system(1)	1	Ovarian(103;0.0398)	all_cancers(173;0.177)|Prostate(94;0.0166)	OV - Ovarian serous cystadenocarcinoma(106;5.43e-05)|Epithelial(3;0.000121)															---	---	---	---
ARID4B	51742	broad.mit.edu	37	1	235328679	235328679	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235328679delT	uc001hwp.2	-							NM_031371				AT rich interactive domain 4B isoform 2						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	235353776	235353776	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235353776delA	uc001hwq.2	-						ARID4B_uc001hwr.2_Intron|ARID4B_uc001hws.3_Intron|ARID4B_uc001hwp.2_Intron|ARID4B_uc001hwt.3_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)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	235510457	235510457	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235510457delA								GGPS1 (2615 upstream) : TBCE (20271 downstream)																																			---	---	---	---
B3GALNT2	148789	broad.mit.edu	37	1	235622455	235622456	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235622455_235622456delAA	uc001hxc.2	-							NM_152490	NP_689703			beta-1,3-N-acetylgalactosaminyltransferase 2						protein glycosylation	Golgi membrane|integral to membrane	galactosyltransferase activity			breast(1)	1	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.0539)|Prostate(94;0.0353)	OV - Ovarian serous cystadenocarcinoma(106;0.000117)															---	---	---	---
LYST	1130	broad.mit.edu	37	1	235875502	235875502	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235875502delA	uc001hxj.2	-						LYST_uc001hxi.2_Intron	NM_000081	NP_000072			lysosomal trafficking regulator						defense response to bacterium|defense response to protozoan|defense response to virus|endosome to lysosome transport via multivesicular body sorting pathway|leukocyte chemotaxis|mast cell secretory granule organization|melanosome organization|natural killer cell mediated cytotoxicity|protein transport	cytoplasm|microtubule cytoskeleton	protein binding			ovary(6)|breast(4)|central_nervous_system(2)	12	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)											Chediak-Higashi_syndrome				---	---	---	---
LYST	1130	broad.mit.edu	37	1	235937120	235937120	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235937120delA	uc001hxj.2	-						LYST_uc009xgb.1_Intron|LYST_uc010pxs.1_Intron	NM_000081	NP_000072			lysosomal trafficking regulator						defense response to bacterium|defense response to protozoan|defense response to virus|endosome to lysosome transport via multivesicular body sorting pathway|leukocyte chemotaxis|mast cell secretory granule organization|melanosome organization|natural killer cell mediated cytotoxicity|protein transport	cytoplasm|microtubule cytoskeleton	protein binding			ovary(6)|breast(4)|central_nervous_system(2)	12	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)											Chediak-Higashi_syndrome				---	---	---	---
EDARADD	128178	broad.mit.edu	37	1	236568967	236568967	+	Intron	DEL	T	-	-	rs34751498		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236568967delT	uc001hxu.1	+						EDARADD_uc001hxv.1_Intron	NM_145861	NP_665860			EDAR-associated death domain isoform A						cell differentiation|signal transduction	cytoplasm					0	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.0232)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)															---	---	---	---
ACTN2	88	broad.mit.edu	37	1	236926030	236926030	+	3'UTR	DEL	A	-	-	rs1051251	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236926030delA	uc001hyf.2	+	21					ACTN2_uc001hyg.2_3'UTR|ACTN2_uc009xgi.1_3'UTR|ACTN2_uc010pxu.1_3'UTR|ACTN2_uc001hyh.2_3'UTR	NM_001103	NP_001094			actinin, alpha 2						focal adhesion assembly|microspike assembly|muscle filament sliding|platelet activation|platelet degranulation|protein homotetramerization|regulation of apoptosis|synaptic transmission	actin filament|cytosol|dendritic spine|extracellular region|filopodium|focal adhesion|nucleolus|platelet alpha granule lumen|pseudopodium|Z disc	actin binding|calcium ion binding|FATZ 1 binding|identical protein binding|integrin binding|protein dimerization activity|structural constituent of muscle|titin binding|titin Z domain binding|ZASP binding			ovary(4)|skin(1)	5	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)															---	---	---	---
MTR	4548	broad.mit.edu	37	1	237025274	237025274	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237025274delA	uc001hyi.3	+						MTR_uc010pxw.1_Intron|MTR_uc010pxx.1_Intron|MTR_uc010pxy.1_Intron	NM_000254	NP_000245			5-methyltetrahydrofolate-homocysteine						nervous system development|xenobiotic metabolic process	cytosol	cobalamin binding|homocysteine S-methyltransferase activity|methionine synthase activity|protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	237188797	237188797	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237188797delT								MTR (121517 upstream) : RYR2 (16905 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	237199220	237199223	+	IGR	DEL	TCCT	-	-	rs66520854		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237199220_237199223delTCCT								MTR (131940 upstream) : RYR2 (6479 downstream)																																			---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237295029	237295030	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237295029_237295030delTT	uc001hyl.1	+							NM_001035	NP_001026			cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)															---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237615285	237615288	+	Intron	DEL	TGTT	-	-	rs66483747		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237615285_237615288delTGTT	uc001hyl.1	+							NM_001035	NP_001026			cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)															---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237659768	237659768	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237659768delT	uc001hyl.1	+							NM_001035	NP_001026			cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)															---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237875200	237875200	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237875200delT	uc001hyl.1	+						RYR2_uc010pxz.1_Intron	NM_001035	NP_001026			cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	238003169	238003170	+	IGR	INS	-	A	A	rs138147909	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238003169_238003170insA								RYR2 (5881 upstream) : LOC100130331 (22305 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	239191837	239191839	+	IGR	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239191837_239191839delTTT								LOC339535 (542520 upstream) : CHRM3 (358026 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	239197938	239197939	+	IGR	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239197938_239197939delCT								LOC339535 (548621 upstream) : CHRM3 (351926 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	239410442	239410442	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239410442delT								LOC339535 (761125 upstream) : CHRM3 (139423 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	240112666	240112666	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240112666delT								CHRM3 (39951 upstream) : FMN2 (142519 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	240240785	240240785	+	IGR	DEL	A	-	-	rs76275694		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240240785delA								CHRM3 (168070 upstream) : FMN2 (14400 downstream)																																			---	---	---	---
FMN2	56776	broad.mit.edu	37	1	240368052	240368052	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240368052delA	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)															---	---	---	---
GREM2	64388	broad.mit.edu	37	1	240656842	240656842	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240656842delT	uc001hys.2	-							NM_022469	NP_071914			gremlin 2 precursor						BMP signaling pathway	extracellular space	cytokine activity				0		all_cancers(173;0.0196)	OV - Ovarian serous cystadenocarcinoma(106;0.0123)															---	---	---	---
RGS7	6000	broad.mit.edu	37	1	241288728	241288729	+	Intron	DEL	AC	-	-	rs67313040		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241288728_241288729delAC	uc001hyv.2	-						RGS7_uc010pyh.1_Intron|RGS7_uc010pyj.1_Intron|RGS7_uc001hyu.2_Intron|RGS7_uc009xgn.1_Intron|RGS7_uc001hyw.2_Intron	NM_002924	NP_002915			regulator of G-protein signaling 7						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|protein binding|signal transducer activity			ovary(4)|skin(2)|kidney(1)	7		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)															---	---	---	---
RGS7	6000	broad.mit.edu	37	1	241407419	241407420	+	Intron	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241407419_241407420delTG	uc001hyv.2	-						RGS7_uc001hyu.2_Intron|RGS7_uc009xgn.1_Intron|RGS7_uc001hyw.2_Intron	NM_002924	NP_002915			regulator of G-protein signaling 7						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|protein binding|signal transducer activity			ovary(4)|skin(2)|kidney(1)	7		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)															---	---	---	---
WDR64	128025	broad.mit.edu	37	1	241873368	241873369	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241873368_241873369delAA	uc001hze.1	+						WDR64_uc001hzf.1_Intron					RecName: Full=WD repeat-containing protein 64;											skin(1)	1	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)															---	---	---	---
WDR64	128025	broad.mit.edu	37	1	241925500	241925502	+	Intron	DEL	GCA	-	-	rs71819425		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241925500_241925502delGCA	uc001hzf.1	+						WDR64_uc001hzg.1_Intron	NM_144625	NP_653226			WD repeat domain 64											skin(1)	1	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	242156490	242156490	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242156490delA								EXO1 (103443 upstream) : MAP1LC3C (2302 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	242181622	242181623	+	IGR	DEL	TT	-	-	rs67509822		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242181622_242181623delTT								MAP1LC3C (19237 upstream) : PLD5 (70649 downstream)																																			---	---	---	---
PLD5	200150	broad.mit.edu	37	1	242312973	242312976	+	Intron	DEL	ACAC	-	-	rs150881263		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242312973_242312976delACAC	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	242693124	242693124	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242693124delC								PLD5 (5126 upstream) : CEP170 (594607 downstream)																																			---	---	---	---
CEP170	9859	broad.mit.edu	37	1	243331955	243331955	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243331955delA	uc001hzs.2	-						CEP170_uc001hzt.2_Intron|CEP170_uc001hzu.2_Intron|CEP170_uc001hzv.1_5'Flank	NM_014812	NP_055627			centrosomal protein 170kDa isoform alpha							centriole|microtubule|spindle				ovary(1)|haematopoietic_and_lymphoid_tissue(1)	2	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	244028294	244028294	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244028294delA								AKT3 (21741 upstream) : ZNF238 (186267 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	244064611	244064611	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244064611delT								AKT3 (58058 upstream) : ZNF238 (149950 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	244302968	244302969	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244302968_244302969delTT								ZNF238 (82192 upstream) : C1orf100 (212968 downstream)																																			---	---	---	---
C1orf101	257044	broad.mit.edu	37	1	244799602	244799602	+	Intron	DEL	T	-	-	rs66715174		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244799602delT	uc001iam.2	+						C1orf101_uc001ial.2_Intron|C1orf101_uc010pym.1_Intron|C1orf101_uc010pyn.1_Intron	NM_001130957	NP_001124429			hypothetical protein LOC257044 isoform 1							integral to membrane				ovary(1)|breast(1)	2	all_cancers(71;2.99e-05)|all_epithelial(71;0.00015)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0874)|Lung NSC(105;0.121)		all cancers(7;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.001)|GBM - Glioblastoma multiforme(7;0.0154)															---	---	---	---
KIF26B	55083	broad.mit.edu	37	1	245697464	245697465	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245697464_245697465delTT	uc001ibf.1	+						KIF26B_uc010pyq.1_Intron|KIF26B_uc001ibg.1_Intron	NM_018012	NP_060482			kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)															---	---	---	---
KIF26B	55083	broad.mit.edu	37	1	245824292	245824292	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245824292delT	uc001ibf.1	+						KIF26B_uc001ibg.1_Intron|KIF26B_uc001ibh.1_Intron	NM_018012	NP_060482			kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)															---	---	---	---
CNST	163882	broad.mit.edu	37	1	246824282	246824282	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246824282delT	uc001ibp.2	+							NM_152609	NP_689822			hypothetical protein LOC163882 isoform 1						positive regulation of Golgi to plasma membrane protein transport	integral to membrane|plasma membrane|protein complex|trans-Golgi network|transport vesicle	connexin binding				0																		---	---	---	---
ZNF124	7678	broad.mit.edu	37	1	247307269	247307270	+	Intron	DEL	AG	-	-	rs35531017		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247307269_247307270delAG	uc001ici.2	-						uc001ich.2_Intron					Homo sapiens cDNA FLJ30085 fis, clone BGGI12001714, highly similar to Homo sapiens zinc finger protein 124 (HZF-16) (ZNF124), mRNA.						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1	all_cancers(71;5.07e-05)|all_epithelial(71;8.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00739)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	247779752	247779752	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247779752delT								OR2G3 (9936 upstream) : OR13G1 (55668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	247820552	247820552	+	IGR	DEL	T	-	-	rs34457351		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247820552delT								OR2G3 (50736 upstream) : OR13G1 (14868 downstream)																																			---	---	---	---
OR2W3	343171	broad.mit.edu	37	1	248044912	248044913	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248044912_248044913delTT	uc001idp.1	+							NM_001001957	NP_001001957			olfactory receptor, family 2, subfamily W,						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	248596259	248596259	+	IGR	DEL	T	-	-	rs67286515		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248596259delT								OR2T1 (25855 upstream) : OR2T2 (19840 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	248608092	248608093	+	IGR	DEL	AA	-	-	rs71761334		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248608092_248608093delAA								OR2T1 (37688 upstream) : OR2T2 (8006 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	249217620	249217620	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:249217620delT								PGBD2 (4276 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	937062	937063	+	IGR	DEL	TG	-	-	rs140701360		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:937062_937063delTG								TMEM18 (259623 upstream) : SNTG2 (9492 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	1574285	1574286	+	IGR	INS	-	A	A	rs139418488	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1574285_1574286insA								TPO (27787 upstream) : PXDN (61374 downstream)																																			---	---	---	---
PXDN	7837	broad.mit.edu	37	2	1737679	1737679	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1737679delT	uc002qxa.2	-						PXDN_uc002qxb.1_Intron|PXDN_uc002qxc.1_Intron	NM_012293	NP_036425			peroxidasin precursor						extracellular matrix organization|hydrogen peroxide catabolic process|immune response	endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix	extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity			pancreas(6)|ovary(2)	8	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)														---	---	---	---
MYT1L	23040	broad.mit.edu	37	2	1894284	1894284	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1894284delA	uc002qxe.2	-						MYT1L_uc002qxd.2_Intron|MYT1L_uc010ewl.1_Intron	NM_015025	NP_055840			myelin transcription factor 1-like						cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)														---	---	---	---
MYT1L	23040	broad.mit.edu	37	2	1956424	1956424	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1956424delC	uc002qxe.2	-						MYT1L_uc002qxd.2_Intron	NM_015025	NP_055840			myelin transcription factor 1-like						cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)														---	---	---	---
MYT1L	23040	broad.mit.edu	37	2	2271641	2271641	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2271641delA	uc002qxe.2	-						MYT1L_uc002qxd.2_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	4840373	4840374	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4840373_4840374delTT								None (None upstream) : SOX11 (992425 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	6187437	6187437	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6187437delA								LOC400940 (59073 upstream) : CMPK2 (793066 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	6188195	6188195	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6188195delA								LOC400940 (59831 upstream) : CMPK2 (792308 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	6866651	6866651	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6866651delT								LOC400940 (738287 upstream) : CMPK2 (113852 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	6895126	6895126	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6895126delT	uc002qym.1	-											Homo sapiens cDNA FLJ42418 fis, clone BLADE2001987.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	6953160	6953161	+	IGR	INS	-	G	G	rs150620180	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6953160_6953161insG								LOC400940 (824796 upstream) : CMPK2 (27342 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	6953787	6953787	+	IGR	DEL	A	-	-	rs146442477	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6953787delA								LOC400940 (825423 upstream) : CMPK2 (26716 downstream)																																			---	---	---	---
CMPK2	129607	broad.mit.edu	37	2	7001225	7001236	+	Intron	DEL	ACACACACACGC	-	-	rs149134084		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7001225_7001236delACACACACACGC	uc002qyo.2	-						CMPK2_uc010yis.1_Intron|CMPK2_uc010ewv.2_Intron	NM_207315	NP_997198			UMP-CMP kinase 2 precursor						dTDP biosynthetic process	mitochondrion	ATP binding|cytidylate kinase activity|thymidylate kinase activity|UMP kinase activity				0	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
RNF144A	9781	broad.mit.edu	37	2	7059502	7059502	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7059502delT	uc002qys.2	+						RNF144A_uc002qyt.2_Intron|uc002qyr.1_5'Flank	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	7345365	7345365	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7345365delT								RNF144A (161058 upstream) : LOC339788 (717193 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	7592023	7592023	+	IGR	DEL	T	-	-	rs112955523		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7592023delT								RNF144A (407716 upstream) : LOC339788 (470535 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	7995825	7995825	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7995825delA								RNF144A (811518 upstream) : LOC339788 (66733 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	8396662	8396662	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8396662delT	uc010eww.1	-						uc002qyy.1_Intron					Homo sapiens cDNA FLJ45673 fis, clone D9OST2003989.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	9272390	9272390	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9272390delT								MBOAT2 (128514 upstream) : ASAP2 (74504 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	9288769	9288769	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9288769delA								MBOAT2 (144893 upstream) : ASAP2 (58125 downstream)																																			---	---	---	---
ITGB1BP1	9270	broad.mit.edu	37	2	9554563	9554563	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9554563delA	uc002qzj.2	-						ITGB1BP1_uc002qzk.2_Intron|ITGB1BP1_uc002qzl.2_Intron|ITGB1BP1_uc002qzm.2_Intron|ITGB1BP1_uc010yiy.1_Intron|ITGB1BP1_uc002qzn.1_Intron	NM_004763	NP_004754			integrin cytoplasmic domain-associated protein 1						cell migration|cell-matrix adhesion|intracellular protein kinase cascade	cytosol|lamellipodium|membrane|ruffle	protein binding|protein binding				0	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.23)														---	---	---	---
CPSF3	51692	broad.mit.edu	37	2	9579950	9579950	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9579950delA	uc002qzo.1	+						CPSF3_uc010ewx.1_Intron|CPSF3_uc002qzp.1_Intron	NM_016207	NP_057291			cleavage and polyadenylation specific factor 3,						histone mRNA 3'-end processing|mRNA cleavage|mRNA export from nucleus|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex|ribonucleoprotein complex	5'-3' exonuclease activity|endoribonuclease activity|metal ion binding|protein binding|RNA binding			breast(2)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;2.39e-25)|all_epithelial(98;8.75e-19)|Lung NSC(108;2.38e-06)|Ovarian(717;0.0308)		all cancers(51;2.2e-40)|Epithelial(75;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(76;4.35e-21)|STAD - Stomach adenocarcinoma(1183;0.00644)														---	---	---	---
HPCAL1	3241	broad.mit.edu	37	2	10485030	10485031	+	Intron	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10485030_10485031delTC	uc002raj.2	+						HPCAL1_uc002rak.2_Intron|HPCAL1_uc002ral.2_Intron|HPCAL1_uc010exe.2_Intron	NM_002149	NP_002140			hippocalcin-like 1								calcium ion binding			pancreas(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.214)														---	---	---	---
HPCAL1	3241	broad.mit.edu	37	2	10540898	10540899	+	Intron	INS	-	AC	AC	rs148235775	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10540898_10540899insAC	uc002raj.2	+						HPCAL1_uc002rak.2_Intron|HPCAL1_uc002ral.2_Intron|HPCAL1_uc010exe.2_Intron|HPCAL1_uc010exf.2_Intron	NM_002149	NP_002140			hippocalcin-like 1								calcium ion binding			pancreas(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.214)														---	---	---	---
ATP6V1C2	245973	broad.mit.edu	37	2	10922664	10922664	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10922664delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	11109052	11109054	+	IGR	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11109052_11109054delTTT								KCNF1 (54702 upstream) : C2orf50 (164125 downstream)																																			---	---	---	---
GREB1	9687	broad.mit.edu	37	2	11776888	11776893	+	Intron	DEL	GGGCAG	-	-	rs70955812		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11776888_11776893delGGGCAG	uc002rbk.1	+						GREB1_uc002rbp.1_Intron	NM_014668	NP_055483			growth regulation by estrogen in breast cancer 1							integral to membrane				ovary(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	12150708	12150709	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12150708_12150709delAA	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	13980607	13980607	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:13980607delT								None (None upstream) : FAM84A (792249 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	14278744	14278745	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:14278744_14278745delAA								None (None upstream) : FAM84A (494111 downstream)																																			---	---	---	---
NBAS	51594	broad.mit.edu	37	2	15565286	15565287	+	Intron	INS	-	A	A	rs143677242	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15565286_15565287insA	uc002rcc.1	-						NBAS_uc010exl.1_5'Flank|NBAS_uc002rcd.1_Intron	NM_015909	NP_056993			neuroblastoma-amplified protein											ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	17371790	17371790	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17371790delA								FAM49A (524694 upstream) : RAD51AP2 (320196 downstream)																																			---	---	---	---
VSNL1	7447	broad.mit.edu	37	2	17744344	17744344	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17744344delA	uc002rcm.2	+							NM_003385	NP_003376			visinin-like 1								calcium ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)																	---	---	---	---
SMC6	79677	broad.mit.edu	37	2	17860044	17860044	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17860044delA	uc002rco.2	-						SMC6_uc010exo.2_Intron|SMC6_uc002rcn.2_Intron	NM_001142286	NP_001135758			SMC6 protein						DNA recombination|DNA repair	chromosome|nucleus	ATP binding			breast(4)|upper_aerodigestive_tract(1)|kidney(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)																	---	---	---	---
SMC6	79677	broad.mit.edu	37	2	17870405	17870406	+	Intron	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17870405_17870406delAG	uc002rco.2	-						SMC6_uc010exo.2_Intron|SMC6_uc002rcn.2_Intron	NM_001142286	NP_001135758			SMC6 protein						DNA recombination|DNA repair	chromosome|nucleus	ATP binding			breast(4)|upper_aerodigestive_tract(1)|kidney(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	18451132	18451132	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18451132delT								KCNS3 (336908 upstream) : NT5C1B (284859 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	18946855	18946855	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18946855delT								NT5C1B (176017 upstream) : OSR1 (604392 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	19067561	19067562	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19067561_19067562delTT								NT5C1B (296723 upstream) : OSR1 (483685 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	19741964	19741965	+	IGR	INS	-	CT	CT	rs150067895	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19741964_19741965insCT								OSR1 (183592 upstream) : TTC32 (354553 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	19791078	19791079	+	IGR	INS	-	TACTAGTAGCAG	TACTAGTAGCAG	rs140002065	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19791078_19791079insTACTAGTAGCAG								OSR1 (232706 upstream) : TTC32 (305439 downstream)																																			---	---	---	---
WDR35	57539	broad.mit.edu	37	2	20141611	20141611	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20141611delA	uc002rdi.2	-						WDR35_uc002rdj.2_Intron|WDR35_uc010ext.2_Intron|WDR35_uc002rdh.2_Intron|WDR35_uc002rdk.3_Intron	NM_001006657	NP_001006658			WD repeat domain 35 isoform 1											ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
WDR35	57539	broad.mit.edu	37	2	20177941	20177942	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20177941_20177942delAC	uc002rdi.2	-						WDR35_uc002rdj.2_Intron|WDR35_uc010ext.2_Intron|WDR35_uc002rdh.2_5'Flank	NM_001006657	NP_001006658			WD repeat domain 35 isoform 1											ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
PUM2	23369	broad.mit.edu	37	2	20526999	20527000	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20526999_20527000delAA	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)																	---	---	---	---
C2orf43	60526	broad.mit.edu	37	2	20884151	20884152	+	3'UTR	DEL	TT	-	-	rs71774243		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20884151_20884152delTT	uc002rea.1	-	9					C2orf43_uc002reb.1_RNA	NM_021925	NP_068744			hypothetical protein LOC60526												0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	22083523	22083523	+	IGR	DEL	A	-	-	rs112516723		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:22083523delA								APOB (816578 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	22663340	22663340	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:22663340delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	23071117	23071117	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23071117delA								None (None upstream) : KLHL29 (684338 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	23408036	23408037	+	IGR	INS	-	C	C	rs149945028	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23408036_23408037insC								None (None upstream) : KLHL29 (347418 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	23492935	23492936	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23492935_23492936delTT								None (None upstream) : KLHL29 (262519 downstream)																																			---	---	---	---
UBXN2A	165324	broad.mit.edu	37	2	24175786	24175786	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24175786delT	uc010exy.2	+						UBXN2A_uc002rem.2_Intron|UBXN2A_uc002ren.2_Intron|UBXN2A_uc010ykj.1_Intron	NM_181713	NP_859064			UBX domain containing 4												0																		---	---	---	---
SF3B14	51639	broad.mit.edu	37	2	24290462	24290462	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24290462delA	uc002rev.2	-	4					SF3B14_uc010eyb.2_RNA	NM_016047	NP_057131			splicing factor 3B, 14 kDa subunit						nuclear mRNA splicing, via spliceosome	nucleoplasm|U12-type spliceosomal complex	nucleotide binding|protein binding|RNA binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
NCOA1	8648	broad.mit.edu	37	2	24805090	24805090	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24805090delT	uc002rfk.2	+						NCOA1_uc010eye.2_Intron|NCOA1_uc002rfi.2_Intron|NCOA1_uc002rfj.2_5'Flank|NCOA1_uc002rfl.2_5'Flank	NM_003743	NP_003734			nuclear receptor coactivator 1 isoform 1										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								---	---	---	---
NCOA1	8648	broad.mit.edu	37	2	24949704	24949705	+	Intron	DEL	AA	-	-	rs71960773		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24949704_24949705delAA	uc002rfk.2	+						NCOA1_uc010eye.2_Intron|NCOA1_uc002rfi.2_Intron|NCOA1_uc002rfj.2_Intron|NCOA1_uc002rfl.2_Intron	NM_003743	NP_003734			nuclear receptor coactivator 1 isoform 1										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								---	---	---	---
ADCY3	109	broad.mit.edu	37	2	25047759	25047759	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25047759delA	uc002rfs.3	-						ADCY3_uc002rfr.3_Intron|ADCY3_uc010ykm.1_Intron	NM_004036	NP_004027			adenylate cyclase 3						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|sensory perception of smell|synaptic transmission|transmembrane transport|water transport	cytoplasm|integral to plasma membrane	ATP binding|calmodulin binding|metal ion binding			breast(3)|ovary(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)																	---	---	---	---
DTNB	1838	broad.mit.edu	37	2	25696551	25696551	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25696551delA	uc002rgh.2	-						DTNB_uc002rgg.2_Intron|DTNB_uc010yko.1_Intron|DTNB_uc010ykp.1_Intron|DTNB_uc002rgo.2_Intron|DTNB_uc002rgi.2_Intron|DTNB_uc002rgj.2_Intron|DTNB_uc002rgk.2_Intron|DTNB_uc002rgl.2_Intron|DTNB_uc002rgq.2_Intron|DTNB_uc002rgm.2_Intron|DTNB_uc002rgn.2_Intron|DTNB_uc002rgr.1_Intron|DTNB_uc010ykq.1_Intron	NM_021907	NP_068707			dystrobrevin, beta isoform 1							cytoplasm	calcium ion binding|zinc ion binding			large_intestine(2)|ovary(2)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
DTNB	1838	broad.mit.edu	37	2	25722051	25722052	+	Intron	DEL	AA	-	-	rs79832178		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25722051_25722052delAA	uc002rgh.2	-						DTNB_uc010yko.1_Intron|DTNB_uc010ykp.1_Intron|DTNB_uc002rgo.2_Intron|DTNB_uc002rgi.2_Intron|DTNB_uc002rgj.2_Intron|DTNB_uc002rgk.2_Intron|DTNB_uc002rgl.2_Intron|DTNB_uc002rgq.2_Intron|DTNB_uc002rgm.2_Intron|DTNB_uc002rgn.2_Intron|DTNB_uc002rgr.1_Intron|DTNB_uc010ykq.1_Intron	NM_021907	NP_068707			dystrobrevin, beta isoform 1							cytoplasm	calcium ion binding|zinc ion binding			large_intestine(2)|ovary(2)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	25944772	25944773	+	IGR	DEL	GA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25944772_25944773delGA								DTNB (48269 upstream) : ASXL2 (17480 downstream)																																			---	---	---	---
ASXL2	55252	broad.mit.edu	37	2	25976269	25976270	+	Intron	DEL	AA	-	-	rs77542986		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25976269_25976270delAA	uc002rgs.2	-						ASXL2_uc002rgt.1_Intron	NM_018263	NP_060733			additional sex combs like 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|protein binding			pancreas(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	26210561	26210561	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26210561delA								KIF3C (5118 upstream) : RAB10 (46168 downstream)																																			---	---	---	---
HADHB	3032	broad.mit.edu	37	2	26468132	26468133	+	Intron	DEL	GT	-	-	rs143481127		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26468132_26468133delGT	uc002rgz.2	+						HADHB_uc010yku.1_Intron|HADHB_uc010ykv.1_Intron|HADHB_uc010ykw.1_Intron|HADHB_uc002rha.2_Intron|HADHA_uc002rgy.2_5'Flank|HADHA_uc010yks.1_5'Flank|HADHA_uc010ykt.1_5'Flank	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)																	---	---	---	---
EPT1	85465	broad.mit.edu	37	2	26575182	26575182	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26575182delT	uc010ykz.1	+						EPT1_uc010eyl.1_Intron	NM_033505	NP_277040			selenoprotein I						phospholipid biosynthetic process	integral to membrane	ethanolaminephosphotransferase activity|metal ion binding				0																		---	---	---	---
RBKS	64080	broad.mit.edu	37	2	28065746	28065746	+	Intron	DEL	T	-	-	rs78190424		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28065746delT	uc002rlo.1	-						RBKS_uc010ezi.1_Intron|RBKS_uc010ymg.1_Intron	NM_022128	NP_071411			ribokinase						D-ribose metabolic process		ATP binding|ribokinase activity			ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
BRE	9577	broad.mit.edu	37	2	28464370	28464370	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28464370delT	uc002rlr.2	+						BRE_uc002rlp.1_Intron|BRE_uc002rlq.2_Intron|BRE_uc002rls.2_Intron|BRE_uc002rlt.2_Intron|BRE_uc002rlu.2_Intron|BRE_uc002rlv.2_Intron	NM_199194	NP_954664			brain and reproductive organ-expressed (TNFRSF1A						apoptosis|chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of anti-apoptosis|positive regulation of DNA repair|response to ionizing radiation|signal transduction	BRCA1-A complex|BRISC complex|cytoplasm|nuclear ubiquitin ligase complex	peroxisome targeting sequence binding|polyubiquitin binding|tumor necrosis factor receptor binding			lung(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
FOSL2	2355	broad.mit.edu	37	2	28632601	28632601	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28632601delT	uc002rma.2	+						FOSL2_uc010ymi.1_Intron	NM_005253	NP_005244			FOS-like antigen 2						cell death|regulation of transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|breast(1)	3	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
PLB1	151056	broad.mit.edu	37	2	28722752	28722752	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28722752delA	uc002rmb.1	+						PLB1_uc010ezj.1_Intron	NM_153021	NP_694566			phospholipase B1 precursor						lipid catabolic process|retinoid metabolic process|steroid metabolic process	apical plasma membrane|integral to membrane	lysophospholipase activity|phospholipase A2 activity|retinyl-palmitate esterase activity			ovary(4)|large_intestine(2)|skin(2)|breast(1)	9	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
PPP1CB	5500	broad.mit.edu	37	2	29004571	29004571	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29004571delT	uc002rmg.2	+						PPP1CB_uc010ymj.1_Intron|PPP1CB_uc010ymk.1_Intron|PPP1CB_uc010yml.1_Intron|PPP1CB_uc002rmh.2_Intron|SPDYA_uc002rmi.2_5'Flank	NM_206876	NP_996759			protein phosphatase 1, catalytic subunit, beta						cell cycle|cell division|glycogen metabolic process|triglyceride catabolic process	MLL5-L complex|nucleolus|PTW/PP1 phosphatase complex	metal ion binding|myosin phosphatase activity|myosin-light-chain-phosphatase activity|protein binding			skin(1)	1	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	29103832	29103832	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29103832delT								TRMT61B (10657 upstream) : WDR43 (13701 downstream)																																			---	---	---	---
FAM179A	165186	broad.mit.edu	37	2	29268413	29268413	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29268413delT	uc010ezl.2	+						FAM179A_uc010ymm.1_Intron|FAM179A_uc002rmr.3_Intron|FAM179A_uc002rms.1_3'UTR	NM_199280	NP_954974			hypothetical protein LOC165186								binding			ovary(3)|skin(1)	4																		---	---	---	---
ALK	238	broad.mit.edu	37	2	29694607	29694608	+	Intron	DEL	TT	-	-	rs112148653		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29694607_29694608delTT	uc002rmy.2	-							NM_004304	NP_004295			anaplastic lymphoma kinase precursor						protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				---	---	---	---
ALK	238	broad.mit.edu	37	2	29723430	29723430	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29723430delT	uc002rmy.2	-							NM_004304	NP_004295			anaplastic lymphoma kinase precursor						protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				---	---	---	---
ALK	238	broad.mit.edu	37	2	30141917	30141918	+	Intron	DEL	CA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30141917_30141918delCA	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	30587413	30587414	+	IGR	INS	-	C	C	rs143240106	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30587413_30587414insC								LBH (104514 upstream) : LCLAT1 (82709 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	31086788	31086788	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31086788delA								CAPN13 (56477 upstream) : GALNT14 (46546 downstream)																																			---	---	---	---
XDH	7498	broad.mit.edu	37	2	31600308	31600308	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31600308delA	uc002rnv.1	-							NM_000379	NP_000370			xanthine dehydrogenase						purine nucleotide catabolic process|xanthine catabolic process	cytosol|extracellular region|peroxisome	2 iron, 2 sulfur cluster binding|electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|molybdopterin cofactor binding|protein homodimerization activity|xanthine dehydrogenase activity|xanthine oxidase activity			skin(4)|breast(2)|ovary(1)|central_nervous_system(1)	8	Acute lymphoblastic leukemia(172;0.155)				Allopurinol(DB00437)|Carvedilol(DB01136)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Desflurane(DB01189)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|NADH(DB00157)|Nitrofurazone(DB00336)|Papaverine(DB01113)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Rasburicase(DB00049)|Spermine(DB00127)|Trifluoperazine(DB00831)|Vitamin E(DB00163)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	32846983	32846983	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32846983delA								BIRC6 (3020 upstream) : TTC27 (6116 downstream)																																			---	---	---	---
RASGRP3	25780	broad.mit.edu	37	2	33709604	33709604	+	Intron	DEL	T	-	-	rs67385313		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33709604delT	uc002rox.2	+						RASGRP3_uc010ync.1_Intron	NM_170672	NP_733772			RAS guanyl releasing protein 3 (calcium and						MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|guanyl-nucleotide exchange factor activity|protein binding|Rap GTPase activator activity|signal transducer activity			lung(3)|ovary(1)|pancreas(1)	5	all_hematologic(175;0.115)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	34166722	34166723	+	IGR	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34166722_34166723delCT								MYADML (213438 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	34335078	34335079	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34335078_34335079delTT								MYADML (381794 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	34490441	34490442	+	IGR	DEL	AA	-	-	rs77338824		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34490441_34490442delAA								MYADML (537157 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	34505174	34505174	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34505174delA								MYADML (551890 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	34613909	34613909	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34613909delA								MYADML (660625 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	35742699	35742699	+	IGR	DEL	C	-	-	rs138573946		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35742699delC								None (None upstream) : CRIM1 (840698 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	35846134	35846134	+	IGR	DEL	A	-	-	rs112106654		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35846134delA								None (None upstream) : CRIM1 (737263 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	36396902	36396902	+	IGR	DEL	A	-	-	rs72223572		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36396902delA								None (None upstream) : CRIM1 (186495 downstream)																																			---	---	---	---
CRIM1	51232	broad.mit.edu	37	2	36639456	36639457	+	Intron	INS	-	AAT	AAT	rs144590172	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36639456_36639457insAAT	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)																---	---	---	---
FEZ2	9637	broad.mit.edu	37	2	36785668	36785668	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36785668delA	uc002rph.2	-						FEZ2_uc002rpe.2_Intron|FEZ2_uc002rpf.2_Intron|FEZ2_uc002rpg.2_Intron|FEZ2_uc002rpi.2_Intron|FEZ2_uc002rpj.2_Intron	NM_005102	NP_005093			zygin 2 isoform 1						axon guidance|signal transduction		protein binding			ovary(1)	1		all_hematologic(82;0.21)																---	---	---	---
FEZ2	9637	broad.mit.edu	37	2	36804405	36804408	+	Intron	DEL	TTTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36804405_36804408delTTTT	uc002rph.2	-						FEZ2_uc002rpe.2_Intron|FEZ2_uc002rpf.2_Intron|FEZ2_uc002rpg.2_Intron|FEZ2_uc002rpi.2_Intron|FEZ2_uc002rpj.2_Intron	NM_005102	NP_005093			zygin 2 isoform 1						axon guidance|signal transduction		protein binding			ovary(1)	1		all_hematologic(82;0.21)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	36893910	36893910	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36893910delA								FEZ2 (68578 upstream) : VIT (30004 downstream)																																			---	---	---	---
CCDC75	253635	broad.mit.edu	37	2	37315480	37315480	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37315480delA	uc010ezz.2	+						CCDC75_uc002rpr.3_Intron	NM_174931	NP_777591			coiled-coil domain containing 75							intracellular	nucleic acid binding				0		all_hematologic(82;0.21)																---	---	---	---
CEBPZ	10153	broad.mit.edu	37	2	37438027	37438027	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37438027delC	uc002rpz.2	-							NM_005760	NP_005751			CCAAT/enhancer binding protein zeta						regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	DNA binding			pancreas(1)	1		all_hematologic(82;0.21)																---	---	---	---
CEBPZ	10153	broad.mit.edu	37	2	37454908	37454908	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37454908delT	uc002rpz.2	-	2	1458	c.1428delA	c.(1426-1428)AAAfs	p.K476fs		NM_005760	NP_005751	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein zeta	476					regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	DNA binding			pancreas(1)	1		all_hematologic(82;0.21)																---	---	---	---
C2orf56	55471	broad.mit.edu	37	2	37465738	37465738	+	Intron	DEL	A	-	-	rs11680401	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37465738delA	uc002rqa.3	+						C2orf56_uc010ynj.1_Intron|C2orf56_uc002rqc.3_Intron|C2orf56_uc010ynk.1_Intron|C2orf56_uc010ynl.1_Intron|C2orf56_uc010fah.2_5'Flank	NM_144736	NP_653337			hypothetical protein LOC55471 isoform 1						mitochondrial respiratory chain complex I assembly	mitochondrion	enzyme binding|methyltransferase activity			central_nervous_system(1)	1		all_hematologic(82;0.21)																---	---	---	---
PRKD3	23683	broad.mit.edu	37	2	37509918	37509918	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37509918delC	uc002rqd.2	-						PRKD3_uc002rqf.1_Intron	NM_005813	NP_005804			protein kinase D3						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction	cytoplasm|membrane|nucleus	ATP binding|metal ion binding|protein binding|protein kinase C activity			lung(2)|ovary(1)|central_nervous_system(1)	4		all_hematologic(82;0.21)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	38001580	38001580	+	IGR	DEL	G	-	-	rs33927711		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38001580delG								CDC42EP3 (102254 upstream) : FAM82A1 (150882 downstream)																																			---	---	---	---
FAM82A1	151393	broad.mit.edu	37	2	38154074	38154075	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38154074_38154075delAA	uc002rql.2	+						FAM82A1_uc002rqk.1_Intron	NM_144713	NP_653314			family with sequence similarity 82, member A1							cytoplasm|integral to membrane|microtubule|spindle pole	binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	38643787	38643787	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38643787delA								ATL2 (39355 upstream) : HNRPLL (146541 downstream)																																			---	---	---	---
ARHGEF33	100271715	broad.mit.edu	37	2	39146422	39146423	+	5'Flank	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39146422_39146423insT	uc010ynq.1	+							NM_001145451	NP_001138923			DH and coiled-coil domain-containing protein												0																		---	---	---	---
SOS1	6654	broad.mit.edu	37	2	39262297	39262297	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39262297delA	uc002rrk.3	-						SOS1_uc010ynr.1_Intron|SOS1_uc002rrj.3_Intron|SOS1_uc002rrl.2_Intron	NM_005633	NP_005624			son of sevenless homolog 1						apoptosis|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol	DNA binding|protein binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			ovary(4)|breast(3)|lung(2)|central_nervous_system(1)	10		all_hematologic(82;0.21)												Noonan_syndrome				---	---	---	---
CDKL4	344387	broad.mit.edu	37	2	39439757	39439757	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39439757delA	uc002rrm.2	-						CDKL4_uc010fal.1_Intron	NM_001009565	NP_001009565			cyclin-dependent kinase-like 4							cytoplasm	ATP binding|cyclin-dependent protein kinase activity			ovary(1)	1		all_hematologic(82;0.248)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	39723024	39723027	+	Intron	DEL	TTTC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39723024_39723027delTTTC	uc002rrq.2	+						uc002rrr.1_Intron					Homo sapiens cDNA FLJ33477 fis, clone BRAMY2002604.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	40300491	40300492	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40300491_40300492delTT	uc002rrw.2	+											Homo sapiens cDNA clone IMAGE:5223469, partial cds.																														---	---	---	---
SLC8A1	6546	broad.mit.edu	37	2	40450945	40450945	+	Intron	DEL	T	-	-	rs75218831		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40450945delT	uc002rrx.2	-						uc002rrw.2_Intron|SLC8A1_uc002rry.2_Intron|SLC8A1_uc002rrz.2_Intron|SLC8A1_uc002rsa.2_Intron|SLC8A1_uc002rsd.3_Intron|SLC8A1_uc002rsb.1_Intron	NM_021097	NP_066920			solute carrier family 8 (sodium/calcium						cell communication|muscle contraction|platelet activation	integral to plasma membrane	calcium:sodium antiporter activity|calmodulin binding|heat shock protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)													---	---	---	---
SLC8A1	6546	broad.mit.edu	37	2	40580695	40580695	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40580695delA	uc002rrx.2	-						SLC8A1_uc002rry.2_Intron|SLC8A1_uc002rrz.2_Intron|SLC8A1_uc002rsa.2_Intron|SLC8A1_uc002rsd.3_Intron|SLC8A1_uc002rsb.1_Intron	NM_021097	NP_066920			solute carrier family 8 (sodium/calcium						cell communication|muscle contraction|platelet activation	integral to plasma membrane	calcium:sodium antiporter activity|calmodulin binding|heat shock protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	41031163	41031163	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41031163delA								SLC8A1 (291588 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	41956664	41956665	+	IGR	INS	-	AC	AC	rs144248976	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41956664_41956665insAC								None (None upstream) : PKDCC (318496 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	42238341	42238342	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42238341_42238342insT								None (None upstream) : PKDCC (36819 downstream)																																			---	---	---	---
KCNG3	170850	broad.mit.edu	37	2	42690806	42690806	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42690806delT	uc002rsn.2	-						KCNG3_uc002rsm.2_Intron	NM_133329	NP_579875			potassium voltage-gated channel, subfamily G,							endoplasmic reticulum|voltage-gated potassium channel complex	protein binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	43168418	43168418	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43168418delT								HAAO (148667 upstream) : ZFP36L2 (281124 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	43387262	43387262	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43387262delT								HAAO (367511 upstream) : ZFP36L2 (62280 downstream)																																			---	---	---	---
THADA	63892	broad.mit.edu	37	2	43517412	43517415	+	Intron	DEL	TTTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43517412_43517415delTTTT	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	44021481	44021481	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44021481delT	uc002rtk.2	+						DYNC2LI1_uc002rth.2_Intron|DYNC2LI1_uc002rti.2_3'UTR|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)																---	---	---	---
LRPPRC	10128	broad.mit.edu	37	2	44193554	44193554	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44193554delT	uc002rtr.2	-						LRPPRC_uc010yob.1_Intron	NM_133259	NP_573566			leucine-rich PPR motif-containing protein						mitochondrion transport along microtubule|mRNA transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	condensed nuclear chromosome|cytoskeleton|mitochondrial nucleoid|nuclear inner membrane|nuclear outer membrane|nucleoplasm|perinuclear region of cytoplasm	beta-tubulin binding|microtubule binding|RNA binding			ovary(2)|skin(1)	3		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)																---	---	---	---
PPM1B	5495	broad.mit.edu	37	2	44413684	44413684	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44413684delT	uc002rtt.2	+						PPM1B_uc002rts.2_Intron|PPM1B_uc002rtu.2_Intron|PPM1B_uc002rtv.2_Intron|PPM1B_uc002rtw.2_Intron|PPM1B_uc002rtx.2_Intron	NM_002706	NP_002697			protein phosphatase 1B isoform 1						protein dephosphorylation	protein serine/threonine phosphatase complex	magnesium ion binding|manganese ion binding|protein binding|protein serine/threonine phosphatase activity			kidney(1)|skin(1)	2		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	45049559	45049560	+	IGR	INS	-	T	T	rs111308482		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45049559_45049560insT								C2orf34 (49830 upstream) : SIX3 (119477 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	45055865	45055865	+	IGR	DEL	A	-	-	rs76804832		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45055865delA								C2orf34 (56136 upstream) : SIX3 (113172 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	45477769	45477769	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45477769delT	uc002ruq.2	-											Homo sapiens cDNA FLJ38231 fis, clone FCBBF2004707.																														---	---	---	---
SRBD1	55133	broad.mit.edu	37	2	45645685	45645685	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45645685delA	uc002rus.2	-						SRBD1_uc010yoc.1_Intron	NM_018079	NP_060549			S1 RNA binding domain 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		hydrolase activity, acting on ester bonds|RNA binding			central_nervous_system(1)	1		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)															---	---	---	---
PRKCE	5581	broad.mit.edu	37	2	46346446	46346447	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46346446_46346447delTT	uc002rut.2	+							NM_005400	NP_005391			protein kinase C, epsilon						activation of phospholipase C activity|induction of apoptosis|intracellular signal transduction|nerve growth factor receptor signaling pathway|platelet activation	cytosol|endoplasmic reticulum|plasma membrane	ATP binding|enzyme activator activity|metal ion binding|signal transducer activity			lung(4)|ovary(3)|kidney(1)|breast(1)|large_intestine(1)	10		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)															---	---	---	---
PRKCE	5581	broad.mit.edu	37	2	46357197	46357197	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46357197delT	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)															---	---	---	---
EPAS1	2034	broad.mit.edu	37	2	46604005	46604005	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46604005delC	uc002ruv.2	+						EPAS1_uc002ruw.2_5'Flank	NM_001430	NP_001421			endothelial PAS domain protein 1						angiogenesis|myoblast cell fate commitment|positive regulation of transcription from RNA polymerase II promoter|response to hypoxia	transcription factor complex	histone acetyltransferase binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|signal transducer activity|transcription coactivator activity|transcription factor binding			ovary(1)|skin(1)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	LUSC - Lung squamous cell carcinoma(58;0.151)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	46665157	46665157	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46665157delA	uc002rux.2	+											Homo sapiens cDNA clone IMAGE:5272141.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	46902038	46902038	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46902038delT								CRIPT (49158 upstream) : SOCS5 (24061 downstream)																																			---	---	---	---
TTC7A	57217	broad.mit.edu	37	2	47144125	47144125	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47144125delA	uc002rvm.2	+						MCFD2_uc002rvk.2_5'Flank|MCFD2_uc002rvl.2_5'Flank|MCFD2_uc010fba.2_Intron|MCFD2_uc010yof.1_Intron	NM_020458	NP_065191			tetratricopeptide repeat domain 7A								binding			breast(1)|skin(1)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)															---	---	---	---
EPCAM	4072	broad.mit.edu	37	2	47600582	47600582	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47600582delT	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				---	---	---	---
Unknown	0	broad.mit.edu	37	2	47618148	47618149	+	IGR	INS	-	A	A	rs140448279	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47618148_47618149insA								EPCAM (3983 upstream) : MSH2 (12057 downstream)																																			---	---	---	---
MSH2	4436	broad.mit.edu	37	2	47789951	47789952	+	Intron	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47789951_47789952delAG	uc002rvz.2	+						KCNK12_uc002rwb.2_Intron	NM_000251	NP_000242			mutS homolog 2						B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes	MutSalpha complex|MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding			large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1)	55		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)					D|Mis|N|F|S		colorectal|endometrial|ovarian	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	2	48181024	48181024	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48181024delA								FBXO11 (48210 upstream) : FOXN2 (360771 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	48437828	48437828	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48437828delC								FBXO11 (305014 upstream) : FOXN2 (103967 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	48499977	48499977	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48499977delA								FBXO11 (367163 upstream) : FOXN2 (41818 downstream)																																			---	---	---	---
FOXN2	3344	broad.mit.edu	37	2	48584644	48584645	+	Intron	DEL	TT	-	-	rs113343294		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48584644_48584645delTT	uc002rwh.1	+							NM_002158	NP_002149			T-cell leukemia virus enhancer factor						embryo 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				0		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.0272)|LUSC - Lung squamous cell carcinoma(58;0.036)															---	---	---	---
NRXN1	9378	broad.mit.edu	37	2	50439605	50439605	+	Intron	DEL	T	-	-	rs113283870		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50439605delT	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	50693641	50693641	+	Intron	DEL	A	-	-	rs78516173	byFrequency;by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50693641delA	uc010fbq.2	-						NRXN1_uc002rxb.3_Intron|NRXN1_uc002rxe.3_Intron|NRXN1_uc002rxc.1_Intron	NM_001135659	NP_001129131			neurexin 1 isoform alpha2 precursor						angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	51714595	51714595	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51714595delA								NRXN1 (454921 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	51771552	51771553	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51771552_51771553delAA								NRXN1 (511878 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	53096433	53096434	+	IGR	DEL	TT	-	-	rs11322292		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53096433_53096434delTT								None (None upstream) : ASB3 (800684 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	53194228	53194228	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53194228delT								None (None upstream) : ASB3 (702890 downstream)																																			---	---	---	---
ACYP2	98	broad.mit.edu	37	2	54511724	54511724	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54511724delT	uc002rxq.3	+							NM_138448	NP_612457			acylphosphatase 2						phosphate metabolic process		acylphosphatase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	54621607	54621607	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54621607delA								C2orf73 (32893 upstream) : SPTBN1 (61847 downstream)																																			---	---	---	---
SPTBN1	6711	broad.mit.edu	37	2	54705048	54705048	+	Intron	DEL	A	-	-	rs77383921		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54705048delA	uc002rxu.2	+						SPTBN1_uc002rxv.1_Intron	NM_003128	NP_003119			spectrin, beta, non-erythrocytic 1 isoform 1						actin filament capping|axon guidance	cytosol|nucleolus|plasma membrane|sarcomere|spectrin	actin binding|calmodulin binding|protein binding|structural constituent of cytoskeleton			ovary(3)|breast(2)|central_nervous_system(2)|skin(1)	8			Lung(47;0.24)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	54905281	54905281	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54905281delT								SPTBN1 (6699 upstream) : EML6 (46868 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	55685523	55685523	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55685523delT								CCDC88A (38466 upstream) : CCDC104 (61217 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	56006787	56006788	+	IGR	DEL	AC	-	-	rs77813663		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56006787_56006788delAC								PNPT1 (85776 upstream) : EFEMP1 (86315 downstream)																																			---	---	---	---
EFEMP1	2202	broad.mit.edu	37	2	56107814	56107814	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56107814delT	uc002rzh.2	-						EFEMP1_uc002rzi.2_Intron|EFEMP1_uc002rzj.2_Intron|EFEMP1_uc010ypc.1_Intron	NM_004105	NP_004096			EGF-containing fibulin-like extracellular matrix						negative regulation of chondrocyte differentiation|peptidyl-tyrosine phosphorylation|regulation of transcription, DNA-dependent|visual perception	extracellular space|proteinaceous extracellular matrix	calcium ion binding|epidermal growth factor receptor activity|epidermal growth factor receptor binding|growth factor activity			ovary(4)|pancreas(1)|skin(1)	6			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	56920040	56920040	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56920040delT								CCDC85A (306732 upstream) : None (None downstream)																																			---	---	---	---
VRK2	7444	broad.mit.edu	37	2	58362151	58362151	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58362151delA	uc002rzo.2	+						VRK2_uc010fcb.2_Intron|VRK2_uc002rzs.2_Intron|VRK2_uc002rzr.2_Intron|VRK2_uc010fcc.2_Intron|VRK2_uc002rzv.2_Intron|VRK2_uc010fcd.2_Intron|VRK2_uc002rzp.2_Intron|VRK2_uc010ypg.1_Intron|VRK2_uc002rzq.2_Intron|VRK2_uc002rzu.2_Intron|VRK2_uc002rzt.2_Intron	NM_001130482	NP_001123954			vaccinia related kinase 2 isoform 2							integral to membrane	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	58771837	58771837	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58771837delT	uc002rzy.2	+											Homo sapiens cDNA FLJ30838 fis, clone FEBRA2002399.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	58844515	58844515	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58844515delA	uc002rzy.2	+											Homo sapiens cDNA FLJ30838 fis, clone FEBRA2002399.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	59115217	59115217	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:59115217delT	uc002rzy.2	+						uc002rzz.2_Intron					Homo sapiens cDNA FLJ30838 fis, clone FEBRA2002399.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	59463572	59463573	+	IGR	DEL	GA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:59463572_59463573delGA								FANCL (995057 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	60206820	60206820	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60206820delT								None (None upstream) : BCL11A (471483 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	60214017	60214018	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60214017_60214018insA								None (None upstream) : BCL11A (464285 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	60580825	60580825	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60580825delT								None (None upstream) : BCL11A (97478 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	60793058	60793058	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60793058delA								BCL11A (12425 upstream) : PAPOLG (190325 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	60894598	60894598	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60894598delA								BCL11A (113965 upstream) : PAPOLG (88785 downstream)																																			---	---	---	---
USP34	9736	broad.mit.edu	37	2	61459673	61459673	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61459673delA	uc002sbe.2	-						USP34_uc002sbf.2_Intron	NM_014709	NP_055524			ubiquitin specific protease 34						positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)															---	---	---	---
USP34	9736	broad.mit.edu	37	2	61532455	61532455	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61532455delA	uc002sbe.2	-							NM_014709	NP_055524			ubiquitin specific protease 34						positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)															---	---	---	---
COMMD1	150684	broad.mit.edu	37	2	62162958	62162958	+	Intron	DEL	T	-	-	rs112285857		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62162958delT	uc002sbp.2	+							NM_152516	NP_689729			MURR1						copper ion homeostasis|negative regulation of NF-kappaB transcription factor activity|positive regulation of protein ubiquitination|regulation of proteasomal ubiquitin-dependent protein catabolic process	cell junction|Cul2-RING ubiquitin ligase complex|cytoplasm|nucleolus	copper ion binding|protein homodimerization activity			ovary(1)	1	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;4.73e-07)|Epithelial(17;0.0216)|all cancers(80;0.0934)															---	---	---	---
EHBP1	23301	broad.mit.edu	37	2	63121529	63121530	+	Intron	DEL	GA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63121529_63121530delGA	uc002sby.2	+						EHBP1_uc010fcp.2_Intron|EHBP1_uc002sbz.2_Intron|EHBP1_uc002scb.2_Intron	NM_015252	NP_056067			EH domain binding protein 1 isoform 1							cytoplasm|membrane				ovary(1)|breast(1)	2	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)											Hereditary_Prostate_Cancer				---	---	---	---
EHBP1	23301	broad.mit.edu	37	2	63148684	63148684	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63148684delA	uc002sby.2	+						EHBP1_uc010fcp.2_Intron|EHBP1_uc002sbz.2_Intron|EHBP1_uc002scb.2_Intron	NM_015252	NP_056067			EH domain binding protein 1 isoform 1							cytoplasm|membrane				ovary(1)|breast(1)	2	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)											Hereditary_Prostate_Cancer				---	---	---	---
C2orf86	51057	broad.mit.edu	37	2	63419516	63419516	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63419516delA	uc002sch.2	-						C2orf86_uc002sce.2_Intron|C2orf86_uc002scf.2_Intron|C2orf86_uc010ypu.1_Intron|C2orf86_uc002scg.2_Intron	NM_015910	NP_056994			hypothetical protein LOC51057 isoform 2						cilium morphogenesis|regulation of embryonic cell shape|regulation of protein localization|septin cytoskeleton organization	cilium axoneme|cytoplasm|cytoskeleton|plasma membrane					0																		---	---	---	---
C2orf86	51057	broad.mit.edu	37	2	63610291	63610291	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63610291delA	uc002sch.2	-						C2orf86_uc002sce.2_Intron|C2orf86_uc002scf.2_Intron|C2orf86_uc010ypu.1_Intron|C2orf86_uc002scg.2_Intron|C2orf86_uc002sci.1_Intron	NM_015910	NP_056994			hypothetical protein LOC51057 isoform 2						cilium morphogenesis|regulation of embryonic cell shape|regulation of protein localization|septin cytoskeleton organization	cilium axoneme|cytoplasm|cytoskeleton|plasma membrane					0																		---	---	---	---
VPS54	51542	broad.mit.edu	37	2	64168462	64168462	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64168462delG	uc002scq.2	-						VPS54_uc002scp.2_Intron|VPS54_uc010fct.2_Intron	NM_016516	NP_057600			vacuolar protein sorting 54 isoform 1						protein transport|retrograde transport, endosome to Golgi						0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	64660396	64660396	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64660396delT								PELI1 (288791 upstream) : HSPC159 (20931 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	64937258	64937258	+	IGR	DEL	T	-	-	rs76653631		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64937258delT								SERTAD2 (56212 upstream) : SLC1A4 (278321 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	65427331	65427332	+	IGR	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65427331_65427332delAG								RAB1A (69896 upstream) : ACTR2 (27497 downstream)																																			---	---	---	---
SPRED2	200734	broad.mit.edu	37	2	65651762	65651762	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65651762delA	uc002sdr.3	-						SPRED2_uc010fcx.1_Intron	NM_181784	NP_861449			sprouty-related protein with EVH-1 domain 2						inactivation of MAPK activity|multicellular organismal development	transport vesicle membrane	stem cell factor receptor binding			ovary(1)|lung(1)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	66331968	66331968	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66331968delA								SPRED2 (672312 upstream) : MEIS1 (330564 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	66652715	66652716	+	IGR	DEL	CA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66652715_66652716delCA								SPRED2 (993059 upstream) : MEIS1 (9816 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	66943179	66943180	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66943179_66943180delTG								MEIS1 (143289 upstream) : ETAA1 (681262 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	67204693	67204693	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67204693delT								MEIS1 (404803 upstream) : ETAA1 (419749 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	67239012	67239013	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67239012_67239013delAA								MEIS1 (439122 upstream) : ETAA1 (385429 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	68209959	68209960	+	IGR	INS	-	A	A	rs143858376	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68209959_68209960insA								ETAA1 (572426 upstream) : C1D (59373 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	68249374	68249375	+	IGR	INS	-	A	A	rs149278910	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68249374_68249375insA								ETAA1 (611841 upstream) : C1D (19958 downstream)																																			---	---	---	---
ARHGAP25	9938	broad.mit.edu	37	2	69016169	69016169	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69016169delT	uc002seu.2	+						ARHGAP25_uc010yqk.1_Intron|ARHGAP25_uc010fdg.2_Intron|ARHGAP25_uc010yql.1_Intron|ARHGAP25_uc002sev.2_Intron|ARHGAP25_uc002sew.2_Intron|ARHGAP25_uc002sex.2_Intron|ARHGAP25_uc010fdh.1_Intron	NM_001007231	NP_001007232			Rho GTPase activating protein 25 isoform a						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(2)|breast(2)	4																		---	---	---	---
NFU1	27247	broad.mit.edu	37	2	69627838	69627838	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69627838delT	uc002sfk.2	-						NFU1_uc002sfj.2_Intron|NFU1_uc002sfl.2_Intron|NFU1_uc002sfm.2_Intron|NFU1_uc010fdi.2_Intron|NFU1_uc002sfn.1_Intron	NM_001002755	NP_001002755			HIRA interacting protein 5 isoform 2						iron-sulfur cluster assembly	cytosol|mitochondrion|nucleus	4 iron, 4 sulfur cluster binding|iron ion binding|protein binding				0																		---	---	---	---
NFU1	27247	broad.mit.edu	37	2	69650601	69650601	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69650601delA	uc002sfk.2	-						NFU1_uc002sfj.2_Intron|NFU1_uc002sfl.2_Intron|NFU1_uc002sfm.2_Intron|NFU1_uc010fdi.2_Intron|NFU1_uc002sfn.1_Intron	NM_001002755	NP_001002755			HIRA interacting protein 5 isoform 2						iron-sulfur cluster assembly	cytosol|mitochondrion|nucleus	4 iron, 4 sulfur cluster binding|iron ion binding|protein binding				0																		---	---	---	---
NFU1	27247	broad.mit.edu	37	2	69652323	69652323	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69652323delA	uc002sfk.2	-						NFU1_uc002sfj.2_Intron|NFU1_uc002sfl.2_Intron|NFU1_uc002sfm.2_Intron|NFU1_uc010fdi.2_Intron|NFU1_uc002sfn.1_Intron	NM_001002755	NP_001002755			HIRA interacting protein 5 isoform 2						iron-sulfur cluster assembly	cytosol|mitochondrion|nucleus	4 iron, 4 sulfur cluster binding|iron ion binding|protein binding				0																		---	---	---	---
ANXA4	307	broad.mit.edu	37	2	70030916	70030916	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70030916delA	uc002sfr.3	+						ANXA4_uc010yqn.1_Intron|ANXA4_uc002sfs.3_Intron|ANXA4_uc010yqo.1_Intron	NM_001153	NP_001144			annexin IV						anti-apoptosis|signal transduction	cytoplasm	calcium ion binding|calcium-dependent phospholipid binding|phospholipase inhibitor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	70176387	70176390	+	IGR	DEL	GAAT	-	-	rs71397383		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70176387_70176390delGAAT								MXD1 (6313 upstream) : ASPRV1 (10836 downstream)																																			---	---	---	---
ASPRV1	151516	broad.mit.edu	37	2	70284371	70284372	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70284371_70284372insA	uc002sga.2	-						uc002sgb.1_Intron|uc002sgc.2_5'Flank|uc002sgd.2_Intron|uc002sge.1_Intron					Homo sapiens cDNA FLJ32260 fis, clone PROST1000334.						protein maturation by peptide bond cleavage|skin development		aspartic-type endopeptidase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	70556691	70556692	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70556691_70556692delAC								FAM136A (27471 upstream) : TGFA (117727 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	71275446	71275446	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71275446delT								OR7E91P (18388 upstream) : NAGK (19962 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	71468544	71468544	+	IGR	DEL	T	-	-	rs78920905		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71468544delT								PAIP2B (14311 upstream) : ZNF638 (35179 downstream)																																			---	---	---	---
ZNF638	27332	broad.mit.edu	37	2	71532587	71532587	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71532587delT	uc010yqw.1	+						ZNF638_uc010fec.2_Intron	NM_014497	NP_055312			zinc finger protein 638						RNA splicing	cytoplasm|nuclear speck	double-stranded DNA binding|nucleotide binding|RNA binding|zinc ion binding			pancreas(2)|ovary(1)|skin(1)	4																		---	---	---	---
DYSF	8291	broad.mit.edu	37	2	71708859	71708862	+	Intron	DEL	TGCT	-	-	rs72038137		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71708859_71708862delTGCT	uc002sie.2	+						DYSF_uc010feg.2_Intron|DYSF_uc010feh.2_Intron|DYSF_uc002sig.3_Intron|DYSF_uc010yqx.1_Intron|DYSF_uc010fee.2_Intron|DYSF_uc010fef.2_Intron|DYSF_uc010fei.2_Intron|DYSF_uc010fek.2_Intron|DYSF_uc010fej.2_Intron|DYSF_uc010fel.2_Intron|DYSF_uc010feo.2_Intron|DYSF_uc010fem.2_Intron|DYSF_uc010fen.2_Intron|DYSF_uc002sif.2_Intron	NM_003494	NP_003485			dysferlin isoform 8							cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	71961788	71961791	+	IGR	DEL	TGTG	-	-	rs113094343		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71961788_71961791delTGTG								DYSF (47896 upstream) : CYP26B1 (394576 downstream)																																			---	---	---	---
EXOC6B	23233	broad.mit.edu	37	2	72528945	72528945	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72528945delT	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	72793142	72793142	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72793142delT	uc010fep.2	-						EXOC6B_uc002sij.2_Intron	NM_015189	NP_056004			SEC15-like 2						protein transport|vesicle docking involved in exocytosis	exocyst				central_nervous_system(2)	2																		---	---	---	---
EXOC6B	23233	broad.mit.edu	37	2	72958237	72958237	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72958237delA	uc010fep.2	-						EXOC6B_uc002sij.2_Intron	NM_015189	NP_056004			SEC15-like 2						protein transport|vesicle docking involved in exocytosis	exocyst				central_nervous_system(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	73098940	73098940	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73098940delA								EXOC6B (45763 upstream) : SPR (15572 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	73554459	73554459	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73554459delT								EGR4 (33630 upstream) : ALMS1 (58427 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	73864933	73864934	+	IGR	INS	-	A	A	rs77050578		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73864933_73864934insA								ALMS1 (27887 upstream) : NAT8 (2916 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	73945965	73945965	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73945965delA								NAT8B (17498 upstream) : TPRKB (10992 downstream)																																			---	---	---	---
TPRKB	51002	broad.mit.edu	37	2	73959835	73959835	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73959835delA	uc002sjn.2	-						TPRKB_uc002sjm.2_Intron|TPRKB_uc002sjl.2_Intron|TPRKB_uc002sjo.2_Intron|TPRKB_uc010yrm.1_Intron	NM_016058	NP_057142			TP53RK binding protein						protein catabolic process	cytosol|nucleus	protein kinase binding			ovary(1)|skin(1)	2																		---	---	---	---
BOLA3	388962	broad.mit.edu	37	2	74374648	74374648	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74374648delT	uc002skc.1	-						BOLA3_uc002skd.1_Intron|uc002ske.2_5'Flank|uc002skf.2_5'Flank|uc002skg.2_5'Flank	NM_212552	NP_997717			bolA-like 3 isoform 1							extracellular region					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	74414106	74414106	+	IGR	DEL	T	-	-	rs111536374		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74414106delT								MOBKL1B (8111 upstream) : MTHFD2 (11584 downstream)																																			---	---	---	---
LBX2	85474	broad.mit.edu	37	2	74730913	74730913	+	5'Flank	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74730913delG	uc002slw.2	-						LOC151534_uc002slx.2_RNA	NM_001009812	NP_001009812			ladybird homeobox 2							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
HTRA2	27429	broad.mit.edu	37	2	74757473	74757473	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74757473delG	uc002smi.1	+	1	942	c.340delG	c.(340-342)GGGfs	p.G114fs	AUP1_uc002sme.2_5'Flank|AUP1_uc002smf.2_5'Flank|AUP1_uc002smg.2_5'Flank|AUP1_uc002smh.2_5'Flank|AUP1_uc010yrx.1_5'Flank|AUP1_uc010yry.1_5'Flank|HTRA2_uc002smj.1_Frame_Shift_Del_p.G114fs|HTRA2_uc002smk.1_Frame_Shift_Del_p.G114fs|HTRA2_uc002sml.1_Frame_Shift_Del_p.G114fs|HTRA2_uc002smm.1_Intron|HTRA2_uc002smn.1_Intron|HTRA2_uc010ffl.2_5'Flank	NM_013247	NP_037379	O43464	HTRA2_HUMAN	HtrA serine peptidase 2 isoform 1 preproprotein	114	Helical; (Potential).				apoptosis|proteolysis|response to stress	CD40 receptor complex|endoplasmic reticulum membrane|internal side of plasma membrane|mitochondrial intermembrane space|mitochondrial membrane|nucleus	serine-type endopeptidase activity|unfolded protein binding			ovary(1)	1																		---	---	---	---
HK2	3099	broad.mit.edu	37	2	75091642	75091642	+	Intron	DEL	T	-	-	rs142770768		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75091642delT	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																		---	---	---	---
TACR1	6869	broad.mit.edu	37	2	75429380	75429380	+	5'Flank	DEL	A	-	-	rs34374747	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75429380delA	uc002sng.2	-						TACR1_uc002snh.2_5'Flank	NM_001058	NP_001049			tachykinin receptor 1 isoform long						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|detection of abiotic stimulus|mechanosensory behavior	integral to plasma membrane	protein binding			ovary(1)	1					Aprepitant(DB00673)|Ketamine(DB01221)|Vapreotide(DB04894)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	76113232	76113232	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76113232delT								C2orf3 (175121 upstream) : LRRTM4 (861626 downstream)																																			---	---	---	---
LRRTM4	80059	broad.mit.edu	37	2	77017446	77017446	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:77017446delT	uc002snr.2	-						LRRTM4_uc002snq.2_Intron	NM_001134745	NP_001128217			leucine rich repeat transmembrane neuronal 4							integral to membrane				pancreas(3)|ovary(1)	4				Colorectal(11;0.059)														---	---	---	---
LRRTM4	80059	broad.mit.edu	37	2	77056444	77056444	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:77056444delA	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	78472797	78472798	+	Intron	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:78472797_78472798delAG	uc002snu.3	-											Homo sapiens cDNA clone IMAGE:4816654.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	79127133	79127133	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79127133delT								SNAR-H (944981 upstream) : REG3G (125693 downstream)																																			---	---	---	---
CTNNA2	1496	broad.mit.edu	37	2	79707867	79707868	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79707867_79707868insT	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	79751675	79751676	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79751675_79751676delAC	uc010yse.1	+						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	81097210	81097210	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:81097210delA								CTNNA2 (221306 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	81284677	81284677	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:81284677delT								CTNNA2 (408773 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	81896312	81896315	+	IGR	DEL	GTGA	-	-	rs71950655	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:81896312_81896315delGTGA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	82088936	82088936	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:82088936delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	82479049	82479049	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:82479049delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	83006727	83006729	+	IGR	DEL	TGT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:83006727_83006729delTGT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	83087625	83087626	+	IGR	INS	-	AT	AT	rs72543268	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:83087625_83087626insAT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	83642937	83642937	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:83642937delT								None (None upstream) : FUNDC2P2 (874869 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	84562022	84562022	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84562022delA								FUNDC2P2 (42698 upstream) : SUCLG1 (88632 downstream)																																			---	---	---	---
SUCLG1	8802	broad.mit.edu	37	2	84676962	84676962	+	Intron	DEL	A	-	-	rs77955793		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84676962delA	uc002son.2	-						SUCLG1_uc010ysk.1_Intron	NM_003849	NP_003840			succinate-CoA ligase, GDP-forming alpha subunit						tricarboxylic acid cycle		ATP citrate synthase activity|GTP binding|succinate-CoA ligase (GDP-forming) activity				0					Succinic acid(DB00139)													---	---	---	---
SUCLG1	8802	broad.mit.edu	37	2	84677140	84677140	+	Intron	DEL	A	-	-	rs2364906	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84677140delA	uc002son.2	-						SUCLG1_uc010ysk.1_Intron	NM_003849	NP_003840			succinate-CoA ligase, GDP-forming alpha subunit						tricarboxylic acid cycle		ATP citrate synthase activity|GTP binding|succinate-CoA ligase (GDP-forming) activity				0					Succinic acid(DB00139)													---	---	---	---
DNAH6	1768	broad.mit.edu	37	2	84989855	84989855	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84989855delT	uc010fgb.2	+						DNAH6_uc002sot.2_Intron	NM_001370	NP_001361			dynein, axonemal, heavy polypeptide 6						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			central_nervous_system(1)	1																		---	---	---	---
DNAH6	1768	broad.mit.edu	37	2	85007904	85007904	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85007904delT	uc010fgb.2	+						DNAH6_uc002sot.2_Intron	NM_001370	NP_001361			dynein, axonemal, heavy polypeptide 6						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			central_nervous_system(1)	1																		---	---	---	---
C2orf89	129293	broad.mit.edu	37	2	85082566	85082566	+	Intron	DEL	A	-	-	rs112200775		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85082566delA	uc010ysl.1	-						C2orf89_uc002sou.3_Intron|C2orf89_uc010fgc.1_Intron	NM_001080824	NP_001074293			hypothetical protein LOC129293 precursor							integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	85315635	85315635	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85315635delA								KCMF1 (29041 upstream) : TCF7L1 (45099 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	86058109	86058112	+	IGR	DEL	TGTG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86058109_86058112delTGTG								ATOH8 (39604 upstream) : ST3GAL5 (8159 downstream)																																			---	---	---	---
POLR1A	25885	broad.mit.edu	37	2	86291287	86291287	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86291287delT	uc002sqs.2	-						POLR1A_uc010ytb.1_Intron	NM_015425	NP_056240			DNA-directed RNA polymerase I A						termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	DNA-directed RNA polymerase I complex|nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|protein binding|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
REEP1	65055	broad.mit.edu	37	2	86498441	86498441	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86498441delA	uc002srh.3	-						REEP1_uc010ytg.1_Intron|REEP1_uc010yth.1_Intron|REEP1_uc010yti.1_Intron	NM_022912	NP_075063			receptor accessory protein 1 isoform 2						cell death|protein insertion into membrane	integral to membrane|mitochondrial membrane	olfactory receptor binding				0																		---	---	---	---
KDM3A	55818	broad.mit.edu	37	2	86678113	86678114	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86678113_86678114insA	uc002sri.3	+						KDM3A_uc010ytj.1_Intron|KDM3A_uc010ytk.1_Intron	NM_018433	NP_060903			jumonji domain containing 1A						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																		---	---	---	---
KDM3A	55818	broad.mit.edu	37	2	86702198	86702198	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86702198delT	uc002sri.3	+						KDM3A_uc010ytj.1_Intron|KDM3A_uc010ytk.1_Intron	NM_018433	NP_060903			jumonji domain containing 1A						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																		---	---	---	---
KDM3A	55818	broad.mit.edu	37	2	86705979	86705980	+	Intron	INS	-	AG	AG			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86705979_86705980insAG	uc002sri.3	+						KDM3A_uc010ytj.1_Intron|KDM3A_uc010ytk.1_Intron	NM_018433	NP_060903			jumonji domain containing 1A						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																		---	---	---	---
VPS24	51652	broad.mit.edu	37	2	86759398	86759398	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86759398delT	uc002srj.2	-						VPS24_uc002srk.2_Intron|VPS24_uc002srl.2_Intron|VPS24_uc010ytl.1_Intron	NM_016079	NP_057163			vacuolar protein sorting 24 isoform 1						cell cycle|cell division|cellular membrane organization|endosome transport|protein transport	cytosol|late endosome membrane	protein binding			central_nervous_system(1)	1																		---	---	---	---
VPS24	51652	broad.mit.edu	37	2	86760633	86760633	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86760633delT	uc002srj.2	-						VPS24_uc002srk.2_Intron|VPS24_uc002srl.2_Intron|VPS24_uc010ytl.1_Intron	NM_016079	NP_057163			vacuolar protein sorting 24 isoform 1						cell cycle|cell division|cellular membrane organization|endosome transport|protein transport	cytosol|late endosome membrane	protein binding			central_nervous_system(1)	1																		---	---	---	---
RMND5A	64795	broad.mit.edu	37	2	87051115	87051116	+	Intron	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87051115_87051116delTG	uc002srs.3	+						CD8B_uc002srw.2_Intron|CD8B_uc002srx.2_Intron|CD8B_uc002sry.2_Intron|CD8B_uc010fgt.2_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	87123377	87123377	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87123377delT	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	88533164	88533164	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88533164delG								THNSL2 (47019 upstream) : FOXI3 (214562 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	88640649	88640650	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88640649_88640650insA								THNSL2 (154504 upstream) : FOXI3 (107076 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	88683603	88683604	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88683603_88683604insA								THNSL2 (197458 upstream) : FOXI3 (64122 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	89831333	89831334	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89831333_89831334insT								FLJ40330 (725208 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	90008306	90008307	+	Intron	INS	-	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90008306_90008307insG	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	90011926	90011926	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90011926delT	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	90463965	90463965	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90463965delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	90478381	90478382	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90478381_90478382insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	91739140	91739142	+	IGR	DEL	TCA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91739140_91739142delTCA								None (None upstream) : LOC654342 (66050 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	91898336	91898336	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91898336delA								LOC654342 (50361 upstream) : GGT8P (65032 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	92076694	92076695	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92076694_92076695delTT								GGT8P (106541 upstream) : FKSG73 (52464 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	92082115	92082115	+	IGR	DEL	A	-	-	rs112735325		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92082115delA								GGT8P (111962 upstream) : FKSG73 (47044 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	92259936	92259936	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92259936delT								FKSG73 (129442 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	92263686	92263693	+	IGR	DEL	GAAGGAAA	-	-	rs142950492	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92263686_92263693delGAAGGAAA								FKSG73 (133192 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	92270243	92270265	+	IGR	DEL	GATTCCATTCGATTCCATTCGAA	-	-	rs145325811	by1000genomes;by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92270243_92270265delGATTCCATTCGATTCCATTCGAA								FKSG73 (139749 upstream) : None (None downstream)																																			---	---	---	---
PROM2	150696	broad.mit.edu	37	2	95937605	95937605	+	5'Flank	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95937605delC	uc002suh.1	+						PROM2_uc002sui.2_5'Flank|PROM2_uc002suj.2_5'Flank|PROM2_uc002suk.2_5'Flank|PROM2_uc002sul.2_5'Flank	NM_144707	NP_653308			prominin 2 precursor							apical plasma membrane|basolateral plasma membrane|cilium membrane|integral to membrane|microvillus membrane				ovary(1)	1																		---	---	---	---
KCNIP3	30818	broad.mit.edu	37	2	96048115	96048115	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96048115delC	uc002sup.2	+						KCNIP3_uc002suq.2_Intron	NM_013434	NP_038462			Kv channel interacting protein 3 isoform 1						apoptosis|signal transduction|transcription, DNA-dependent	endoplasmic reticulum|Golgi apparatus|nucleus|plasma membrane	calcium ion binding|DNA binding|potassium channel activity|transcription corepressor activity|voltage-gated ion channel activity			breast(2)|ovary(1)	3				READ - Rectum adenocarcinoma(193;0.13)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	96527713	96527714	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96527713_96527714insA	uc002sva.1	-						uc002suz.1_Intron|uc002svb.1_Intron					Homo sapiens cDNA FLJ41632 fis, clone FCBBF1000297, highly  similar to Human protein immuno-reactive with anti-PTH polyclonal antibodies mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	96761002	96761002	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96761002delA								GPAT2 (59280 upstream) : ADRA2B (17624 downstream)																																			---	---	---	---
STARD7	56910	broad.mit.edu	37	2	96861887	96861887	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96861887delA	uc002svm.3	-						STARD7_uc002svl.2_5'Flank	NM_020151	NP_064536			START domain containing 7 precursor							mitochondrion					0																		---	---	---	---
TMEM131	23505	broad.mit.edu	37	2	98409503	98409503	+	Intron	DEL	A	-	-	rs77004501		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98409503delA	uc002syh.3	-							NM_015348	NP_056163			RW1 protein							integral to membrane				ovary(4)|central_nervous_system(2)	6																		---	---	---	---
TMEM131	23505	broad.mit.edu	37	2	98429454	98429454	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98429454delA	uc002syh.3	-							NM_015348	NP_056163			RW1 protein							integral to membrane				ovary(4)|central_nervous_system(2)	6																		---	---	---	---
TMEM131	23505	broad.mit.edu	37	2	98539080	98539080	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98539080delA	uc002syh.3	-						TMEM131_uc010yvg.1_Intron	NM_015348	NP_056163			RW1 protein							integral to membrane				ovary(4)|central_nervous_system(2)	6																		---	---	---	---
VWA3B	200403	broad.mit.edu	37	2	98792784	98792784	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98792784delC	uc002syo.2	+						VWA3B_uc010yvh.1_Intron|VWA3B_uc002syj.2_Intron|VWA3B_uc002syk.1_Intron|VWA3B_uc002syl.1_Intron|VWA3B_uc002sym.2_Intron|VWA3B_uc002syn.1_Intron|VWA3B_uc010yvi.1_Intron	NM_144992	NP_659429			von Willebrand factor A domain containing 3B											ovary(3)|large_intestine(2)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	99045470	99045470	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99045470delT								CNGA3 (30413 upstream) : INPP4A (15851 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	99215186	99215186	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99215186delA								INPP4A (7691 upstream) : C2orf64 (680 downstream)																																			---	---	---	---
MGAT4A	11320	broad.mit.edu	37	2	99240481	99240482	+	3'UTR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99240481_99240482delTT	uc002sze.2	-	16					C2orf64_uc002sza.2_Intron|MGAT4A_uc010yvm.1_Intron|MGAT4A_uc010fil.2_3'UTR	NM_012214	NP_036346			alpha-1,3-mannosyl-glycoprotein						N-glycan processing|post-translational protein modification|protein N-linked glycosylation via asparagine	extracellular region|Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			skin(1)	1																		---	---	---	---
MGAT4A	11320	broad.mit.edu	37	2	99294369	99294369	+	Intron	DEL	A	-	-	rs34897914		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99294369delA	uc002sze.2	-						MGAT4A_uc010fil.2_Intron	NM_012214	NP_036346			alpha-1,3-mannosyl-glycoprotein						N-glycan processing|post-translational protein modification|protein N-linked glycosylation via asparagine	extracellular region|Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			skin(1)	1																		---	---	---	---
REV1	51455	broad.mit.edu	37	2	100098318	100098318	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100098318delA	uc002tad.2	-						REV1_uc002tac.2_Intron	NM_016316	NP_057400			REV1-like isoform 1						DNA replication|error-prone translesion synthesis|response to UV	nucleoplasm	damaged DNA binding|DNA-directed DNA polymerase activity|magnesium ion binding|protein binding			ovary(2)	2													DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
Unknown	0	broad.mit.edu	37	2	100131512	100131514	+	IGR	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100131512_100131514delAAA								REV1 (25032 upstream) : AFF3 (32204 downstream)																																			---	---	---	---
AFF3	3899	broad.mit.edu	37	2	100299919	100299919	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100299919delT	uc002tag.2	-						AFF3_uc002taf.2_Intron|AFF3_uc010fiq.1_Intron|AFF3_uc010yvr.1_Intron|AFF3_uc002tah.1_Intron	NM_002285	NP_002276			AF4/FMR2 family, member 3 isoform 1						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6																		---	---	---	---
AFF3	3899	broad.mit.edu	37	2	100397797	100397797	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100397797delT	uc002tag.2	-						AFF3_uc002taf.2_Intron|AFF3_uc010fiq.1_Intron|AFF3_uc010yvr.1_Intron|AFF3_uc002tah.1_Intron|AFF3_uc010fir.1_Intron	NM_002285	NP_002276			AF4/FMR2 family, member 3 isoform 1						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	101207094	101207094	+	IGR	DEL	A	-	-	rs55675417		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101207094delA								PDCL3 (13893 upstream) : NPAS2 (229519 downstream)																																			---	---	---	---
TBC1D8	11138	broad.mit.edu	37	2	101708188	101708188	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101708188delA	uc010fiv.2	-						TBC1D8_uc010yvw.1_Intron	NM_001102426	NP_001095896			TBC1 domain family, member 8						blood circulation|positive regulation of cell proliferation	intracellular|membrane	calcium ion binding|Rab GTPase activator activity			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	101834118	101834118	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101834118delA								TBC1D8 (66272 upstream) : C2orf29 (35227 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	102665336	102665336	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102665336delA								IL1R2 (20456 upstream) : IL1R1 (21500 downstream)																																			---	---	---	---
IL1R1	3554	broad.mit.edu	37	2	102699794	102699794	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102699794delT	uc010fix.2	+							NM_000877	NP_000868			interleukin 1 receptor, type I precursor						innate immune response	integral to plasma membrane	interleukin-1, Type I, activating receptor activity|platelet-derived growth factor receptor binding			skin(1)	1					Anakinra(DB00026)													---	---	---	---
IL18R1	8809	broad.mit.edu	37	2	102974342	102974343	+	Intron	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102974342_102974343delGT	uc002tbw.3	+							NM_003855	NP_003846			interleukin 18 receptor 1 precursor						innate immune response	integral to membrane|plasma membrane	interleukin-1 receptor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	103956237	103956237	+	IGR	DEL	A	-	-	rs112816208		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103956237delA								TMEM182 (522101 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	105235452	105235452	+	IGR	DEL	A	-	-	rs68065662		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105235452delA								LOC150568 (106238 upstream) : POU3F3 (236517 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	105866009	105866009	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105866009delA								GPR45 (6085 upstream) : TGFBRAP1 (17533 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	106074565	106074565	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106074565delA								FHL2 (19335 upstream) : NCK2 (286789 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	106270136	106270136	+	IGR	DEL	T	-	-	rs67106943		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106270136delT								FHL2 (214906 upstream) : NCK2 (91218 downstream)																																			---	---	---	---
NCK2	8440	broad.mit.edu	37	2	106510191	106510192	+	3'UTR	INS	-	AAAG	AAAG	rs141829577	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106510191_106510192insAAAG	uc002tdg.2	+	5					NCK2_uc002tdh.2_3'UTR|NCK2_uc002tdi.2_3'UTR	NM_003581	NP_003572			NCK adaptor protein 2 isoform A						axon guidance|epidermal growth factor receptor signaling pathway|negative regulation of cell proliferation|positive regulation of actin filament polymerization|positive regulation of T cell proliferation|regulation of epidermal growth factor receptor activity|regulation of translation|signal complex assembly|T cell activation	cytosol|endoplasmic reticulum	cytoskeletal adaptor activity|receptor signaling complex scaffold activity			ovary(1)|lung(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	106564528	106564529	+	IGR	INS	-	GGAG	GGAG	rs146751303	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106564528_106564529insGGAG								NCK2 (53802 upstream) : C2orf40 (117584 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	106851821	106851821	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106851821delA								UXS1 (41026 upstream) : PLGLA (150948 downstream)																																			---	---	---	---
RGPD3	653489	broad.mit.edu	37	2	107075791	107075791	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107075791delA	uc010ywi.1	-							NM_001144013	NP_001137485			RANBP2-like and GRIP domain containing 3						intracellular transport		binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	107315190	107315190	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107315190delA								RGPD3 (230389 upstream) : ST6GAL2 (102868 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	108224829	108224829	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108224829delA								ST6GAL2 (721266 upstream) : LOC729121 (214691 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	108342989	108342990	+	IGR	DEL	GA	-	-	rs9678081		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108342989_108342990delGA								ST6GAL2 (839426 upstream) : LOC729121 (96530 downstream)																																			---	---	---	---
RGPD4	285190	broad.mit.edu	37	2	108446634	108446634	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108446634delA	uc010ywk.1	+							NM_182588	NP_872394			RANBP2-like and GRIP domain containing 4						intracellular transport		binding			skin(2)	2																		---	---	---	---
GCC2	9648	broad.mit.edu	37	2	109067338	109067338	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109067338delA	uc002tec.2	+						GCC2_uc002ted.2_Intron	NM_181453	NP_852118			GRIP and coiled-coil domain-containing 2						Golgi ribbon formation|late endosome to Golgi transport|microtubule anchoring|microtubule organizing center organization|protein localization in Golgi apparatus|protein targeting to lysosome|recycling endosome to Golgi transport|regulation of protein exit from endoplasmic reticulum	membrane|trans-Golgi network	identical protein binding			ovary(1)	1																		---	---	---	---
LIMS1	3987	broad.mit.edu	37	2	109213277	109213277	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109213277delA	uc002teg.2	+						LIMS1_uc002tef.2_Intron|LIMS1_uc002teh.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	109213684	109213684	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109213684delT	uc002teg.2	+						LIMS1_uc002tef.2_Intron|LIMS1_uc002teh.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																		---	---	---	---
EDAR	10913	broad.mit.edu	37	2	109524512	109524512	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109524512delG	uc002teq.3	-						EDAR_uc010fjn.2_Intron|EDAR_uc010yws.1_Intron	NM_022336	NP_071731			ectodysplasin A receptor precursor						apoptosis|cell differentiation	integral to membrane	protein binding|transmembrane receptor activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	109688130	109688131	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109688130_109688131delAA								EDAR (82302 upstream) : SH3RF3 (57866 downstream)																																			---	---	---	---
SH3RF3	344558	broad.mit.edu	37	2	109962639	109962639	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109962639delT	uc010ywt.1	+							NM_001099289	NP_001092759			SH3 domain containing ring finger 3								zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	110494538	110494538	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110494538delA								ANKRD57 (117975 upstream) : RGPD5 (55797 downstream)																																			---	---	---	---
NPHP1	4867	broad.mit.edu	37	2	110886672	110886672	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110886672delA	uc002tfn.3	-						NPHP1_uc002tfm.3_Intron|NPHP1_uc002tfl.3_Intron|NPHP1_uc002tfo.3_Intron|NPHP1_uc010ywx.1_Intron|NPHP1_uc010fjv.1_Intron	NM_207181	NP_997064			nephrocystin 1 isoform 2						actin cytoskeleton organization|cell projection organization|cell-cell adhesion|excretion|retina development in camera-type eye|signal transduction|spermatid differentiation|visual behavior	adherens junction|cell-cell junction|cilium axoneme|cytoplasm|cytoskeleton|motile cilium|photoreceptor connecting cilium	protein binding|structural molecule activity			ovary(2)	2																		---	---	---	---
NPHP1	4867	broad.mit.edu	37	2	110914358	110914361	+	Intron	DEL	TTTT	-	-	rs72323781		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110914358_110914361delTTTT	uc002tfn.3	-						NPHP1_uc002tfm.3_Intron|NPHP1_uc002tfl.3_Intron|NPHP1_uc002tfo.3_Intron|NPHP1_uc010ywx.1_Intron|NPHP1_uc010fjv.1_Intron	NM_207181	NP_997064			nephrocystin 1 isoform 2						actin cytoskeleton organization|cell projection organization|cell-cell adhesion|excretion|retina development in camera-type eye|signal transduction|spermatid differentiation|visual behavior	adherens junction|cell-cell junction|cilium axoneme|cytoplasm|cytoskeleton|motile cilium|photoreceptor connecting cilium	protein binding|structural molecule activity			ovary(2)	2																		---	---	---	---
ACOXL	55289	broad.mit.edu	37	2	111556087	111556087	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111556087delC	uc002tgr.3	+						ACOXL_uc010fkc.2_Intron|ACOXL_uc010yxk.1_Intron	NM_001105516	NP_001098986			acyl-Coenzyme A oxidase-like 2						fatty acid beta-oxidation	peroxisome	acyl-CoA dehydrogenase activity|acyl-CoA oxidase activity				0																		---	---	---	---
LOC541471	541471	broad.mit.edu	37	2	112252633	112252634	+	RNA	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112252633_112252634delAA	uc002the.2	-	1		c.59_60delTT			LOC541471_uc010yxl.1_RNA|LOC541471_uc002thf.3_RNA					Homo sapiens hypothetical LOC541471, mRNA (cDNA clone IMAGE:3459303).												0																		---	---	---	---
TMEM87B	84910	broad.mit.edu	37	2	112827471	112827471	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112827471delG	uc002thm.2	+						TMEM87B_uc010fkg.2_Intron|TMEM87B_uc010fkh.2_Intron	NM_032824	NP_116213			transmembrane protein 87B precursor							integral to membrane					0																		---	---	---	---
ZC3H8	84524	broad.mit.edu	37	2	112986078	112986080	+	Intron	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112986078_112986080delAAA	uc002thp.2	-							NM_032494	NP_115883			zinc finger CCCH-type containing 8						apoptosis|negative regulation of T cell differentiation in thymus|negative regulation of transcription, DNA-dependent|positive regulation of thymocyte apoptosis|response to antibiotic|T cell homeostasis	nucleus	RNA binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
CKAP2L	150468	broad.mit.edu	37	2	113501396	113501396	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113501396delA	uc002tie.2	-						CKAP2L_uc002tif.2_Intron|CKAP2L_uc010yxp.1_Intron	NM_152515	NP_689728			cytoskeleton associated protein 2-like							centrosome					0																		---	---	---	---
CKAP2L	150468	broad.mit.edu	37	2	113513316	113513316	+	Intron	DEL	A	-	-	rs150191453		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113513316delA	uc002tie.2	-						CKAP2L_uc002tif.2_Intron|CKAP2L_uc010yxp.1_Intron|CKAP2L_uc010yxq.1_Intron	NM_152515	NP_689728			cytoskeleton associated protein 2-like							centrosome					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	113905944	113905945	+	IGR	INS	-	G	G	rs70937206		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113905944_113905945insG								IL1RN (14352 upstream) : PSD4 (25615 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	114433786	114433786	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114433786delT								RABL2A (32812 upstream) : SLC35F5 (38145 downstream)																																			---	---	---	---
SLC35F5	80255	broad.mit.edu	37	2	114475434	114475434	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114475434delA	uc002tku.1	-						SLC35F5_uc002tkt.2_Intron	NM_025181	NP_079457			solute carrier family 35, member F5						transport	integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	114552156	114552159	+	IGR	DEL	GAAG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114552156_114552159delGAAG								SLC35F5 (37756 upstream) : ACTR3 (95378 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	114593536	114593536	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114593536delT								SLC35F5 (79136 upstream) : ACTR3 (54001 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	114617462	114617462	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114617462delA								SLC35F5 (103062 upstream) : ACTR3 (30075 downstream)																																			---	---	---	---
DPP10	57628	broad.mit.edu	37	2	115894236	115894236	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:115894236delA	uc002tla.1	+						DPP10_uc002tlb.1_Intron|DPP10_uc002tlc.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	116871009	116871009	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116871009delT								DPP10 (269073 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	117160285	117160286	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:117160285_117160286insT								DPP10 (558349 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	117391749	117391750	+	IGR	DEL	CA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:117391749_117391750delCA								DPP10 (789813 upstream) : None (None downstream)																																			---	---	---	---
STEAP3	55240	broad.mit.edu	37	2	120023164	120023164	+	3'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120023164delT	uc002tlp.2	+	6					STEAP3_uc002tlq.2_3'UTR|STEAP3_uc002tlr.2_3'UTR|STEAP3_uc010fle.2_3'UTR	NM_018234	NP_060704			dudulin 2 isoform b						apoptosis|cell cycle|cellular iron ion homeostasis|protein secretion|transferrin transport|transmembrane transport	endosome membrane|integral to membrane|multivesicular body	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding			central_nervous_system(2)|skin(1)	3																OREG0014928	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PTPN4	5775	broad.mit.edu	37	2	120515848	120515849	+	5'Flank	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120515848_120515849insT	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	120555744	120555745	+	Intron	INS	-	TT	TT			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120555744_120555745insTT	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	120733300	120733301	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120733300_120733301delAA	uc002tmf.1	+						PTPN4_uc010flj.1_Intron|PTPN4_uc010yyr.1_Intron	NM_002830	NP_002821			protein tyrosine phosphatase, non-receptor type							cytoplasm|cytoskeleton|internal side of plasma membrane	cytoskeletal protein binding|non-membrane spanning protein tyrosine phosphatase activity			ovary(2)	2					Alendronate(DB00630)													---	---	---	---
INHBB	3625	broad.mit.edu	37	2	121108172	121108173	+	3'UTR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121108172_121108173delTG	uc002tmn.2	+	2						NM_002193	NP_002184			inhibin beta B subunit preproprotein						activin receptor signaling pathway|cellular response to insulin stimulus|cellular response to starvation|defense response|fat cell differentiation|growth|negative regulation of follicle-stimulating hormone secretion|negative regulation of hepatocyte growth factor biosynthetic process|negative regulation of insulin secretion|ovarian follicle development|positive regulation of follicle-stimulating hormone secretion|positive regulation of ovulation	extracellular region|perinuclear region of cytoplasm	cytokine activity|growth factor activity|hormone activity|host cell surface receptor binding|protein homodimerization activity			pancreas(2)|skin(1)	3		Prostate(154;0.122)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	121149118	121149118	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121149118delG								INHBB (39735 upstream) : LOC84931 (72793 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	121187638	121187638	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121187638delT								INHBB (78255 upstream) : LOC84931 (34273 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	121837576	121837576	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121837576delT								GLI2 (87348 upstream) : TFCP2L1 (136590 downstream)																																	OREG0014948	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CLASP1	23332	broad.mit.edu	37	2	122201414	122201414	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122201414delA	uc002tnc.2	-						CLASP1_uc002tna.2_Intron|CLASP1_uc010yyw.1_Intron|CLASP1_uc002tnb.2_Intron|CLASP1_uc010yyx.1_Intron|CLASP1_uc010yyy.1_Intron|CLASP1_uc010yyz.1_Intron|CLASP1_uc010yza.1_Intron|CLASP1_uc010yzb.1_Intron|CLASP1_uc010yzc.1_Intron|CLASP1_uc002tng.1_Intron	NM_015282	NP_056097			CLIP-associating protein 1 isoform 1						axon guidance|cell division|establishment or maintenance of cell polarity|exit from mitosis|G2/M transition of mitotic cell cycle|microtubule anchoring|microtubule bundle formation|microtubule nucleation|microtubule organizing center organization|mitotic prometaphase|negative regulation of microtubule depolymerization	centrosomal corona|condensed chromosome kinetochore|cortical microtubule cytoskeleton|cytoplasmic microtubule|cytosol|Golgi apparatus|kinetochore microtubule	kinetochore binding|microtubule plus-end binding			ovary(1)|central_nervous_system(1)	2	Renal(3;0.0496)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	122980857	122980860	+	IGR	DEL	TGAT	-	-	rs3060716		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122980857_122980860delTGAT								TSN (455431 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	123171211	123171220	+	IGR	DEL	GAAGAATGGG	-	-	rs72150750		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:123171211_123171220delGAAGAATGGG								TSN (645785 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	123337795	123337795	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:123337795delA								TSN (812369 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	124405907	124405907	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124405907delT								None (None upstream) : CNTNAP5 (376957 downstream)																																			---	---	---	---
CNTNAP5	129684	broad.mit.edu	37	2	125057209	125057210	+	Intron	INS	-	GT	GT	rs145984368	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125057209_125057210insGT	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	125204770	125204770	+	Intron	DEL	T	-	-	rs112719430		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125204770delT	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	125583676	125583677	+	Intron	DEL	TA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125583676_125583677delTA	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	125594758	125594760	+	Intron	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125594758_125594760delAAA	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	126059273	126059274	+	IGR	DEL	TT	-	-	rs138904577	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126059273_126059274delTT								CNTNAP5 (386412 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	126379790	126379790	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126379790delA								CNTNAP5 (706929 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	127525165	127525166	+	IGR	INS	-	CT	CT	rs138071331	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127525165_127525166insCT								GYPC (70920 upstream) : BIN1 (280441 downstream)																																			---	---	---	---
BIN1	274	broad.mit.edu	37	2	127806031	127806031	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127806031delA	uc002tns.1	-	19					BIN1_uc010yzf.1_3'UTR|BIN1_uc010yzg.1_3'UTR|BIN1_uc002tnu.1_3'UTR|BIN1_uc002toa.1_3'UTR|BIN1_uc002tnt.1_3'UTR|BIN1_uc002tnv.1_3'UTR|BIN1_uc002tnw.1_3'UTR|BIN1_uc002tnx.1_3'UTR|BIN1_uc002tny.1_3'UTR|BIN1_uc002tnz.1_3'UTR|BIN1_uc002tob.1_3'UTR|BIN1_uc002toc.1_3'UTR	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	127984168	127984171	+	IGR	DEL	TCTC	-	-	rs10534211		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127984168_127984171delTCTC								CYP27C1 (20825 upstream) : ERCC3 (30695 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	128007517	128007517	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128007517delA								CYP27C1 (44174 upstream) : ERCC3 (7349 downstream)																																			---	---	---	---
IWS1	55677	broad.mit.edu	37	2	128242573	128242578	+	Intron	DEL	AAAAAG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128242573_128242578delAAAAAG	uc002ton.2	-							NM_017969	NP_060439			IWS1 homolog						transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0735)														---	---	---	---
POLR2D	5433	broad.mit.edu	37	2	128610807	128610807	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128610807delT	uc002tpj.2	-						POLR2D_uc002tpk.2_Intron	NM_004805	NP_004796			DNA directed RNA polymerase II polypeptide D						mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA-directed RNA polymerase activity|nucleotide binding				0	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0675)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	128652564	128652564	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128652564delA								AMMECR1L (9050 upstream) : SAP130 (46227 downstream)																																			---	---	---	---
SAP130	79595	broad.mit.edu	37	2	128728532	128728535	+	Intron	DEL	TTTT	-	-	rs114009223	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128728532_128728535delTTTT	uc002tpp.2	-						SAP130_uc002tpn.2_Intron|SAP130_uc002tpo.2_Intron|SAP130_uc010fmd.2_Intron|SAP130_uc002tpq.1_Intron	NM_024545	NP_078821			Sin3A-associated protein, 130kDa isoform b						histone H3 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	STAGA complex	transcription coactivator activity			ovary(2)|skin(2)	4	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	129151918	129151918	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129151918delT								HS6ST1 (75747 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	129508484	129508484	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129508484delT								HS6ST1 (432313 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	129777775	129777775	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129777775delA								HS6ST1 (701604 upstream) : LOC389033 (902660 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	129931613	129931613	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129931613delA								HS6ST1 (855442 upstream) : LOC389033 (748822 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	130269278	130269278	+	IGR	DEL	A	-	-	rs80289123		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130269278delA								None (None upstream) : LOC389033 (411157 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	130410131	130410132	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130410131_130410132insT								None (None upstream) : LOC389033 (270303 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	130703491	130703491	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130703491delA								LOC389033 (11601 upstream) : RAB6C (33744 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	131000154	131000154	+	IGR	DEL	T	-	-	rs77841472		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131000154delT								TUBA3E (44120 upstream) : CCDC115 (95662 downstream)																																			---	---	---	---
FAM168B	130074	broad.mit.edu	37	2	131830672	131830672	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131830672delT	uc002tsd.2	-							NM_001009993	NP_001009993			hypothetical protein LOC130074												0																		---	---	---	---
TUBA3D	113457	broad.mit.edu	37	2	132238483	132238484	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132238483_132238484insT	uc002tsu.3	+							NM_080386	NP_525125			tubulin, alpha 3d						'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|protein binding|structural molecule activity				0				BRCA - Breast invasive adenocarcinoma(221;0.13)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	132435226	132435226	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132435226delT								CCDC74A (143989 upstream) : C2orf27A (44838 downstream)																																			---	---	---	---
NCRNA00164	554226	broad.mit.edu	37	2	133011694	133011695	+	Intron	INS	-	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133011694_133011695insC	uc002ttj.3	-							NR_027020				Homo sapiens non-protein coding RNA 164, mRNA (cDNA clone IMAGE:5169389), with apparent retained intron.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	133028275	133028278	+	IGR	DEL	AAAG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133028275_133028278delAAAG								NCRNA00164 (12733 upstream) : GPR39 (145869 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	133080904	133080904	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133080904delT								NCRNA00164 (65362 upstream) : GPR39 (93243 downstream)																																			---	---	---	---
NCKAP5	344148	broad.mit.edu	37	2	133442426	133442426	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133442426delA	uc002ttp.2	-						NCKAP5_uc002ttq.2_Intron	NM_207363	NP_997246			Nck-associated protein 5 isoform 1								protein binding				0																		---	---	---	---
NCKAP5	344148	broad.mit.edu	37	2	133644939	133644942	+	Intron	DEL	TCCA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133644939_133644942delTCCA	uc002ttp.2	-						NCKAP5_uc002ttq.2_Intron	NM_207363	NP_997246			Nck-associated protein 5 isoform 1								protein binding				0																		---	---	---	---
NCKAP5	344148	broad.mit.edu	37	2	133984177	133984178	+	Intron	DEL	AC	-	-	rs111493512		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133984177_133984178delAC	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	134037107	134037107	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134037107delT	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	134122682	134122683	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134122682_134122683delAC	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	134851598	134851598	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134851598delG								NCKAP5 (525567 upstream) : MGAT5 (160232 downstream)																																			---	---	---	---
RAB3GAP1	22930	broad.mit.edu	37	2	135867548	135867548	+	Intron	DEL	T	-	-	rs78817708		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135867548delT	uc002tuj.2	+						RAB3GAP1_uc010fnf.2_Intron|RAB3GAP1_uc010fng.2_Intron|RAB3GAP1_uc010fnh.1_Intron	NM_012233	NP_036365			RAB3 GTPase-activating protein							centrosome|nucleus|soluble fraction	Rab GTPase activator activity|Rab GTPase binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.117)														---	---	---	---
ZRANB3	84083	broad.mit.edu	37	2	136047959	136047959	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136047959delT	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	136103039	136103040	+	Intron	DEL	AA	-	-	rs113439308		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136103039_136103040delAA	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	136152306	136152306	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136152306delA	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	136220176	136220176	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136220176delT	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)														---	---	---	---
LCT	3938	broad.mit.edu	37	2	136565836	136565836	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136565836delT	uc002tuu.1	-							NM_002299	NP_002290			lactase-phlorizin hydrolase preproprotein						carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|integral to plasma membrane|membrane fraction	cation binding|glycosylceramidase activity|lactase activity			ovary(7)|central_nervous_system(2)|skin(2)|pancreas(1)|lung(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.169)														---	---	---	---
DARS	1615	broad.mit.edu	37	2	136716544	136716544	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136716544delA	uc002tux.1	-						DARS_uc010fnj.1_Intron	NM_001349	NP_001340			aspartyl-tRNA synthetase						aspartyl-tRNA aminoacylation|protein complex assembly	cytosol|nuclear membrane|plasma membrane|soluble fraction	aminoacylase activity|aspartate-tRNA ligase activity|ATP binding|nucleic acid binding|protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.168)	L-Aspartic Acid(DB00128)													---	---	---	---
THSD7B	80731	broad.mit.edu	37	2	137608952	137608952	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137608952delT	uc010zbj.1	+											Homo sapiens mRNA for KIAA1679 protein, partial cds.											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)														---	---	---	---
THSD7B	80731	broad.mit.edu	37	2	137714256	137714257	+	Intron	DEL	TT	-	-	rs35474378		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137714256_137714257delTT	uc010zbj.1	+											Homo sapiens mRNA for KIAA1679 protein, partial cds.											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)														---	---	---	---
THSD7B	80731	broad.mit.edu	37	2	138334375	138334376	+	Intron	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138334375_138334376delCT	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	138374602	138374602	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138374602delA	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	138996733	138996733	+	IGR	DEL	T	-	-	rs75001840		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138996733delT								HNMT (222800 upstream) : SPOPL (262617 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	140458760	140458761	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140458760_140458761insT								NXPH2 (920949 upstream) : LRP1B (530235 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	140822057	140822057	+	IGR	DEL	A	-	-	rs5834707		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140822057delA								None (None upstream) : LRP1B (166939 downstream)																																			---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	141243422	141243423	+	Intron	INS	-	CACG	CACG	rs141641170	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141243422_141243423insCACG	uc002tvj.1	-							NM_018557	NP_061027			low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)											TSP Lung(27;0.18)			---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	141598364	141598364	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141598364delT	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	141625631	141625631	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141625631delA	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	142011893	142011893	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142011893delA	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)			---	---	---	---
KYNU	8942	broad.mit.edu	37	2	143718078	143718078	+	Intron	DEL	A	-	-	rs74847108		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:143718078delA	uc002tvl.2	+						KYNU_uc002tvk.2_Intron|KYNU_uc010fnm.2_Intron	NM_003937	NP_003928			kynureninase (L-kynurenine hydrolase) isoform a						anthranilate metabolic process|NAD biosynthetic process|quinolinate biosynthetic process|response to interferon-gamma|response to vitamin B6	cytosol|mitochondrion|soluble fraction	kynureninase activity|protein homodimerization activity			skin(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.072)	L-Alanine(DB00160)|Pyridoxal Phosphate(DB00114)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	143807011	143807011	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:143807011delA								KYNU (7127 upstream) : ARHGAP15 (79888 downstream)																																			---	---	---	---
ARHGAP15	55843	broad.mit.edu	37	2	144412981	144412990	+	Intron	DEL	ACTGCCAGAC	-	-	rs140761690		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144412981_144412990delACTGCCAGAC	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)														---	---	---	---
GTDC1	79712	broad.mit.edu	37	2	144949956	144949956	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144949956delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	146530393	146530393	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146530393delT								None (None upstream) : PABPC1P2 (814232 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	146737236	146737236	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146737236delT								None (None upstream) : PABPC1P2 (607389 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	146876585	146876585	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146876585delG								None (None upstream) : PABPC1P2 (468040 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	147799512	147799512	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:147799512delA								PABPC1P2 (450955 upstream) : ACVR2A (802574 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	148453616	148453616	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148453616delG								None (None upstream) : ACVR2A (148470 downstream)																																			---	---	---	---
ACVR2A	92	broad.mit.edu	37	2	148683686	148683686	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148683686delA	uc002twg.2	+	11	1572	c.1303delA	c.(1303-1305)AAAfs	p.K435fs	ACVR2A_uc010zbn.1_Frame_Shift_Del_p.K327fs|ACVR2A_uc002twh.2_Frame_Shift_Del_p.K435fs	NM_001616	NP_001607	P27037	AVR2A_HUMAN	activin A receptor, type IIA precursor	435	Cytoplasmic (Potential).|Protein kinase.				activin receptor signaling pathway|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of erythrocyte differentiation|positive regulation of osteoblast differentiation|positive regulation of protein phosphorylation	cytoplasm|inhibin-betaglycan-ActRII complex|integral to plasma membrane	ATP binding|coreceptor activity|inhibin beta-A binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity			stomach(8)|large_intestine(2)|lung(1)|breast(1)|kidney(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.0969)														---	---	---	---
ORC4L	5000	broad.mit.edu	37	2	148707012	148707012	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148707012delG	uc002twi.2	-						ORC4L_uc002twj.2_Intron|ORC4L_uc010zbo.1_Intron|ORC4L_uc010zbp.1_Intron|ORC4L_uc010fnr.2_Intron|ORC4L_uc010zbq.1_Intron|ORC4L_uc002twk.2_Intron|ORC4L_uc010zbr.1_Intron	NM_181741	NP_859525			origin recognition complex subunit 4						cell cycle checkpoint|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	nuclear origin of replication recognition complex|nucleoplasm	ATP binding|DNA replication origin binding|nucleoside-triphosphatase activity|protein binding				0				BRCA - Breast invasive adenocarcinoma(221;0.0963)|COAD - Colon adenocarcinoma(177;0.203)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	149603875	149603875	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149603875delA								EPC2 (58740 upstream) : KIF5C (28944 downstream)																																			---	---	---	---
KIF5C	3800	broad.mit.edu	37	2	149807944	149807944	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149807944delT	uc010zbu.1	+						KIF5C_uc002tws.1_Intron	NM_004522	NP_004513			kinesin family member 5C						microtubule-based movement|organelle organization	cytoplasm|kinesin complex|microtubule	ATP binding|microtubule motor activity			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.108)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	150359126	150359127	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150359126_150359127delTT								LYPD6 (28989 upstream) : MMADHC (67023 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	150939719	150939719	+	IGR	DEL	G	-	-	rs11333909		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150939719delG								MMADHC (495389 upstream) : RND3 (384993 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	152011547	152011547	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152011547delA								RND3 (667367 upstream) : RBM43 (93182 downstream)																																			---	---	---	---
TNFAIP6	7130	broad.mit.edu	37	2	152214427	152214428	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152214427_152214428delTT	uc002txk.2	+							NM_007115	NP_009046			tumor necrosis factor, alpha-induced protein 6						cell adhesion|cell-cell signaling|inflammatory response|signal transduction		hyaluronic acid binding				0				BRCA - Breast invasive adenocarcinoma(221;0.131)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	152616223	152616223	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152616223delA								NEB (25234 upstream) : ARL5A (29370 downstream)																																			---	---	---	---
CACNB4	785	broad.mit.edu	37	2	152918757	152918757	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152918757delA	uc002tya.2	-						CACNB4_uc002txz.2_Intron|CACNB4_uc010fnz.2_Intron	NM_000726	NP_000717			calcium channel, voltage-dependent, beta 4						axon guidance|membrane depolarization|synaptic transmission	cytosol|internal side of plasma membrane|plasma membrane|synapse|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.156)	Verapamil(DB00661)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	153746276	153746276	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153746276delC								ARL6IP6 (128509 upstream) : RPRM (587576 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	154019841	154019842	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:154019841_154019842insT								ARL6IP6 (402074 upstream) : RPRM (314010 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	154406914	154406914	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:154406914delT								RPRM (71592 upstream) : GALNT13 (321512 downstream)																																			---	---	---	---
GALNT13	114805	broad.mit.edu	37	2	154803957	154803957	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:154803957delT	uc002tyr.3	+						GALNT13_uc002tyt.3_Intron	NM_052917	NP_443149			UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)|pancreas(2)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
GALNT13	114805	broad.mit.edu	37	2	154979406	154979407	+	Intron	DEL	TG	-	-	rs77346617		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:154979406_154979407delTG	uc002tyr.3	+						GALNT13_uc002tyt.3_Intron	NM_052917	NP_443149			UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)|pancreas(2)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
KCNJ3	3760	broad.mit.edu	37	2	155628905	155628905	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155628905delT	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	155824497	155824497	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155824497delA								KCNJ3 (111483 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	156043152	156043152	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:156043152delA								KCNJ3 (330138 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	156317084	156317084	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:156317084delT								KCNJ3 (604070 upstream) : NR4A2 (863862 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	156516464	156516464	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:156516464delT								KCNJ3 (803450 upstream) : NR4A2 (664482 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	156679209	156679209	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:156679209delA								KCNJ3 (966195 upstream) : NR4A2 (501737 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	156693936	156693937	+	IGR	INS	-	A	A	rs147627763	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:156693936_156693937insA								KCNJ3 (980922 upstream) : NR4A2 (487009 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	158061410	158061410	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158061410delT								GPD2 (591163 upstream) : GALNT5 (52930 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	158222214	158222214	+	IGR	DEL	T	-	-	rs66760426		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158222214delT								ERMN (38068 upstream) : CYTIP (48917 downstream)																																			---	---	---	---
PKP4	8502	broad.mit.edu	37	2	159488063	159488063	+	Intron	DEL	T	-	-	rs75092706		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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)			---	---	---	---
Unknown	0	broad.mit.edu	37	2	159813506	159813507	+	IGR	DEL	AG	-	-	rs72060984		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159813506_159813507delAG								DAPL1 (141012 upstream) : TANC1 (11639 downstream)																																			---	---	---	---
BAZ2B	29994	broad.mit.edu	37	2	160454049	160454049	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160454049delT	uc002uao.2	-						BAZ2B_uc002uap.2_Intron|BAZ2B_uc002uas.1_Intron|BAZ2B_uc002uau.1_Intron	NM_013450	NP_038478			bromodomain adjacent to zinc finger domain, 2B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|skin(1)	4																		---	---	---	---
BAZ2B	29994	broad.mit.edu	37	2	160530185	160530186	+	Intron	DEL	AA	-	-	rs112640742		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160530185_160530186delAA	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																		---	---	---	---
BAZ2B	29994	broad.mit.edu	37	2	160557955	160557955	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160557955delT	uc002uau.1	-						uc002uaw.2_Intron					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	160732257	160732257	+	Intron	DEL	A	-	-	rs75237280		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160732257delA	uc002ubc.3	-						LY75_uc002ubb.3_Intron|LY75_uc010fos.2_Intron|LY75_uc010fot.1_Intron	NM_002349	NP_002340			lymphocyte antigen 75 precursor						endocytosis|immune response|inflammatory response	integral to plasma membrane	receptor activity|sugar binding				0				COAD - Colon adenocarcinoma(177;0.132)														---	---	---	---
ITGB6	3694	broad.mit.edu	37	2	161031076	161031077	+	Intron	INS	-	T	T	rs139714864	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161031076_161031077insT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	161366918	161366918	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161366918delA								RBMS1 (16600 upstream) : TANK (626548 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	161734312	161734312	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161734312delA								RBMS1 (383994 upstream) : TANK (259154 downstream)																																			---	---	---	---
IFIH1	64135	broad.mit.edu	37	2	163134716	163134716	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163134716delT	uc002uce.2	-	9	1986	c.1764delA	c.(1762-1764)AAAfs	p.K588fs		NM_022168	NP_071451	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1	588					detection of virus|innate immune response|interspecies interaction between organisms|negative regulation of type I interferon production|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|regulation of apoptosis	cytosol|nucleus	ATP binding|DNA binding|double-stranded RNA binding|helicase activity|protein binding|ribonucleoprotein binding|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	163180876	163180876	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163180876delT								IFIH1 (5837 upstream) : GCA (19707 downstream)																																			---	---	---	---
GCA	25801	broad.mit.edu	37	2	163205885	163205885	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163205885delT	uc002ucg.2	+						GCA_uc010zcu.1_Intron	NM_012198	NP_036330			grancalcin, EF-hand calcium binding protein						cellular membrane fusion	cytoplasm|plasma membrane	calcium ion binding|protein homodimerization activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	164113525	164113525	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:164113525delT								KCNH7 (418285 upstream) : FIGN (350593 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	164382617	164382617	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:164382617delA								KCNH7 (687377 upstream) : FIGN (81501 downstream)																																			---	---	---	---
FIGN	55137	broad.mit.edu	37	2	164584679	164584680	+	Intron	INS	-	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:164584679_164584680insC	uc002uck.1	-							NM_018086	NP_060556			fidgetin							nuclear matrix	ATP binding|nucleoside-triphosphatase activity			large_intestine(2)|ovary(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	165218023	165218023	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165218023delA								FIGN (625510 upstream) : GRB14 (131310 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	165310494	165310494	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165310494delA								FIGN (717981 upstream) : GRB14 (38839 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	165877083	165877084	+	IGR	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165877083_165877084delAG								SLC38A11 (65048 upstream) : SCN3A (66948 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	165890863	165890864	+	IGR	INS	-	AAAC	AAAC	rs140890428	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165890863_165890864insAAAC								SLC38A11 (78828 upstream) : SCN3A (53168 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	165918355	165918355	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165918355delT								SLC38A11 (106320 upstream) : SCN3A (25677 downstream)																																			---	---	---	---
CSRNP3	80034	broad.mit.edu	37	2	166527805	166527805	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166527805delA	uc002udf.2	+						CSRNP3_uc002udg.2_Intron	NM_024969	NP_079245			cysteine-serine-rich nuclear protein 3						apoptosis|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|large_intestine(1)|skin(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	167603405	167603405	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167603405delA								SCN7A (252688 upstream) : XIRP2 (141592 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	168272468	168272468	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168272468delA								XIRP2 (156209 upstream) : B3GALT1 (402714 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	168475455	168475455	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168475455delT								XIRP2 (359196 upstream) : B3GALT1 (199727 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	168505568	168505568	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168505568delT								XIRP2 (389309 upstream) : B3GALT1 (169614 downstream)																																			---	---	---	---
LASS6	253782	broad.mit.edu	37	2	169509297	169509297	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169509297delA	uc002ueb.1	+						LASS6_uc002uec.1_Intron	NM_203463	NP_982288			longevity assurance homolog 6							endoplasmic reticulum membrane|integral to membrane|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity			skin(1)	1																		---	---	---	---
FASTKD1	79675	broad.mit.edu	37	2	170393895	170393895	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170393895delT	uc002uev.3	-						FASTKD1_uc002uew.3_Intron|FASTKD1_uc002uex.3_Intron	NM_024622	NP_078898			FAST kinase domains 1						apoptosis|cellular respiration	mitochondrion	ATP binding|protein kinase activity			ovary(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	170637706	170637706	+	IGR	DEL	T	-	-	rs72016206		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170637706delT								KLHL23 (31268 upstream) : SSB (17683 downstream)																																			---	---	---	---
METTL5	29081	broad.mit.edu	37	2	170680745	170680745	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170680745delA	uc002ufn.2	-						METTL5_uc002ufo.2_Intron|METTL5_uc002ufp.2_Intron|METTL5_uc002ufq.1_Intron	NM_014168	NP_054887			methyltransferase like 5								methyltransferase activity|nucleic acid binding			central_nervous_system(1)	1																		---	---	---	---
UBR3	130507	broad.mit.edu	37	2	170761615	170761615	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170761615delT	uc010zdi.1	+							NM_172070	NP_742067			E3 ubiquitin-protein ligase UBR3						sensory perception of smell|suckling behavior|ubiquitin-dependent protein catabolic process	integral to membrane	ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
UBR3	130507	broad.mit.edu	37	2	170938525	170938525	+	3'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	171625893	171625893	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171625893delA	uc002ugf.1	-											Homo sapiens cDNA FLJ13453 fis, clone PLACE1003205.																														---	---	---	---
GAD1	2571	broad.mit.edu	37	2	171689173	171689176	+	Intron	DEL	CGCA	-	-	rs35212610		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171689173_171689176delCGCA	uc002ugi.2	+						GAD1_uc002ugh.2_Intron	NM_000817	NP_000808			glutamate decarboxylase 1 isoform GAD67						glutamate decarboxylation to succinate|neurotransmitter biosynthetic process|neurotransmitter secretion|protein-pyridoxal-5-phosphate linkage	clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|plasma membrane	glutamate decarboxylase activity|protein binding|pyridoxal phosphate binding			ovary(1)	1					L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)													---	---	---	---
HAT1	8520	broad.mit.edu	37	2	172809273	172809274	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172809273_172809274delTT	uc002uhi.2	+						HAT1_uc010fqi.2_Intron|HAT1_uc002uhj.2_Intron	NM_003642	NP_003633			histone acetyltransferase 1						chromatin silencing at telomere|DNA packaging	cytoplasm|nuclear matrix|nucleoplasm	histone acetyltransferase activity|protein binding			large_intestine(1)|ovary(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.216)															---	---	---	---
RAPGEF4	11069	broad.mit.edu	37	2	173703580	173703581	+	Intron	INS	-	A	A	rs138486048	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173703580_173703581insA	uc002uhv.3	+						RAPGEF4_uc002uhu.2_Intron|RAPGEF4_uc002uhw.3_Intron	NM_007023	NP_008954			Rap guanine nucleotide exchange factor (GEF) 4						blood coagulation|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of insulin secretion|regulation of protein phosphorylation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cAMP-dependent protein kinase complex|membrane fraction|plasma membrane	cAMP binding|cAMP-dependent protein kinase regulator activity|Ras GTPase binding|Ras guanyl-nucleotide exchange factor activity			large_intestine(2)|skin(2)|kidney(1)|central_nervous_system(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.194)															---	---	---	---
RAPGEF4	11069	broad.mit.edu	37	2	173896263	173896263	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173896263delA	uc002uhv.3	+						RAPGEF4_uc002uhw.3_Intron	NM_007023	NP_008954			Rap guanine nucleotide exchange factor (GEF) 4						blood coagulation|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of insulin secretion|regulation of protein phosphorylation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cAMP-dependent protein kinase complex|membrane fraction|plasma membrane	cAMP binding|cAMP-dependent protein kinase regulator activity|Ras GTPase binding|Ras guanyl-nucleotide exchange factor activity			large_intestine(2)|skin(2)|kidney(1)|central_nervous_system(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.194)															---	---	---	---
ZAK	51776	broad.mit.edu	37	2	174023018	174023019	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174023018_174023019insA	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	174332794	174332794	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174332794delT								CDCA7 (99076 upstream) : SP3 (440465 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	174484623	174484624	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174484623_174484624insA								CDCA7 (250905 upstream) : SP3 (288635 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	174656247	174656247	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174656247delG								CDCA7 (422529 upstream) : SP3 (117012 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	174856235	174856236	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174856235_174856236delTC								SP3 (26172 upstream) : OLA1 (80940 downstream)																																			---	---	---	---
GPR155	151556	broad.mit.edu	37	2	175319532	175319533	+	Intron	INS	-	AAGGGAAGGAAGGGAAAGGAAGGAAAGGGA	AAGGGAAGGAAGGGAAAGGAAGGAAAGGGA	rs148035088	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175319532_175319533insAAGGGAAGGAAGGGAAAGGAAGGAAAGGGA	uc002uit.2	-						GPR155_uc002uiu.2_Intron|GPR155_uc002uiv.2_Intron|GPR155_uc010fqs.2_Intron	NM_001033045	NP_001028217			G protein-coupled receptor 155 isoform 9						intracellular signal transduction|transmembrane transport	integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	175584494	175584494	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175584494delT	uc002uiw.2	+											Homo sapiens cDNA FLJ11228 fis, clone PLACE1008329.																												OREG0015078	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CHN1	1123	broad.mit.edu	37	2	175756297	175756297	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175756297delA	uc002uji.2	-						CHN1_uc010zeq.1_Intron|CHN1_uc002ujj.2_Intron	NM_001822	NP_001813			chimerin (chimaerin) 1 isoform a						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(2)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.226)					T	TAF15	extraskeletal myxoid chondrosarcoma								---	---	---	---
CHN1	1123	broad.mit.edu	37	2	175762152	175762153	+	Intron	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175762152_175762153delTG	uc002uji.2	-						CHN1_uc010zeq.1_Intron|CHN1_uc002ujj.2_Intron	NM_001822	NP_001813			chimerin (chimaerin) 1 isoform a						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(2)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.226)					T	TAF15	extraskeletal myxoid chondrosarcoma								---	---	---	---
Unknown	0	broad.mit.edu	37	2	175924516	175924517	+	IGR	INS	-	GT	GT	rs144107894	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175924516_175924517insGT								CHN1 (54346 upstream) : ATF2 (14491 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	176481063	176481063	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176481063delT								ATP5G3 (434573 upstream) : KIAA1715 (309347 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	178033610	178033610	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178033610delA								MIR1246 (567830 upstream) : HNRNPA3 (43812 downstream)																																			---	---	---	---
OSBPL6	114880	broad.mit.edu	37	2	179138463	179138463	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179138463delT	uc002ulx.2	+						OSBPL6_uc002ulw.2_Intron|OSBPL6_uc002uly.2_Intron|OSBPL6_uc010zfe.1_Intron	NM_032523	NP_115912			oxysterol-binding protein-like protein 6 isoform						lipid transport		lipid binding			pancreas(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)															---	---	---	---
OSBPL6	114880	broad.mit.edu	37	2	179156519	179156520	+	Intron	INS	-	CCAT	CCAT			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179156519_179156520insCCAT	uc002ulx.2	+						OSBPL6_uc002ulw.2_Intron|OSBPL6_uc002uly.2_Intron|OSBPL6_uc010zfe.1_Intron|OSBPL6_uc002ulz.2_Intron	NM_032523	NP_115912			oxysterol-binding protein-like protein 6 isoform						lipid transport		lipid binding			pancreas(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)															---	---	---	---
DFNB59	494513	broad.mit.edu	37	2	179321040	179321040	+	Intron	DEL	A	-	-	rs11448490		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179321040delA	uc002umi.3	+						DFNB59_uc002umj.3_Intron	NM_001042702	NP_001036167			deafness, autosomal recessive 59						sensory perception of sound						0			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.0159)|all cancers(119;0.0564)															---	---	---	---
DFNB59	494513	broad.mit.edu	37	2	179325063	179325063	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179325063delT	uc002umi.3	+						DFNB59_uc002umj.3_Intron	NM_001042702	NP_001036167			deafness, autosomal recessive 59						sensory perception of sound						0			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.0159)|all cancers(119;0.0564)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179558767	179558767	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179558767delT	uc010zfg.1	-						TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron|TTN_uc010fre.1_Intron	NM_133378	NP_596869			titin isoform N2-A								ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
CCDC141	285025	broad.mit.edu	37	2	179889834	179889834	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179889834delT	uc002ung.2	-											SubName: Full=Putative uncharacterized protein CCDC141; SubName: Full=Putative uncharacterized protein FLJ39502;								protein binding			ovary(7)|pancreas(2)|skin(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)															---	---	---	---
SESTD1	91404	broad.mit.edu	37	2	180032367	180032367	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180032367delA	uc002uni.3	-							NM_178123	NP_835224			SEC14 and spectrin domains 1						regulation of calcium ion transport via voltage-gated calcium channel activity		phosphatidic acid binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylinositol-4-phosphate binding|phosphatidylinositol-5-phosphate binding|protein binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)															---	---	---	---
SESTD1	91404	broad.mit.edu	37	2	180049287	180049288	+	Intron	DEL	AA	-	-	rs71903758		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180049287_180049288delAA	uc002uni.3	-							NM_178123	NP_835224			SEC14 and spectrin domains 1						regulation of calcium ion transport via voltage-gated calcium channel activity		phosphatidic acid binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylinositol-4-phosphate binding|phosphatidylinositol-5-phosphate binding|protein binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)															---	---	---	---
ZNF385B	151126	broad.mit.edu	37	2	180554943	180554943	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180554943delA	uc002unn.3	-						ZNF385B_uc002unm.2_Intron	NM_152520	NP_689733			zinc finger protein 385B isoform 1							nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	181949051	181949051	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181949051delA								UBE2E3 (20901 upstream) : ITGA4 (372568 downstream)																																			---	---	---	---
CERKL	375298	broad.mit.edu	37	2	182501195	182501195	+	Intron	DEL	A	-	-	rs111429385		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182501195delA	uc002unx.2	-						CERKL_uc002uny.2_Intron|CERKL_uc010zfm.1_Intron|CERKL_uc002unz.2_Intron|CERKL_uc002uoa.2_Intron|CERKL_uc002uob.2_Intron|CERKL_uc002uoc.2_Intron|CERKL_uc010frk.2_Intron|CERKL_uc002uod.1_Intron|CERKL_uc002uoe.2_Intron	NM_001030311	NP_001025482			ceramide kinase-like isoform b						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|anti-apoptosis	endoplasmic reticulum|endoplasmic reticulum|Golgi apparatus|Golgi apparatus|nucleolus|nucleolus	diacylglycerol kinase activity			ovary(2)|kidney(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.088)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	182736917	182736917	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182736917delT								CERKL (191536 upstream) : SSFA2 (19555 downstream)																																			---	---	---	---
SSFA2	6744	broad.mit.edu	37	2	182773585	182773585	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182773585delT	uc002uoi.2	+						SSFA2_uc002uoh.2_Intron|SSFA2_uc002uoj.2_Intron|SSFA2_uc002uok.2_Intron|SSFA2_uc010zfo.1_Intron|SSFA2_uc002uol.2_Intron	NM_001130445	NP_001123917			sperm specific antigen 2 isoform 1							cytoplasm|plasma membrane	actin binding			breast(1)|central_nervous_system(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0856)															---	---	---	---
PPP1R1C	151242	broad.mit.edu	37	2	182983632	182983632	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182983632delT	uc010frm.1	+						PPP1R1C_uc002uon.2_Intron|PPP1R1C_uc002uop.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)															---	---	---	---
PDE1A	5136	broad.mit.edu	37	2	183137437	183137437	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183137437delA	uc002uos.2	-						PDE1A_uc010zfp.1_Intron|PDE1A_uc002uoq.1_Intron|PDE1A_uc010zfq.1_Intron|PDE1A_uc002uor.2_Intron|PDE1A_uc002uov.1_Intron	NM_001003683	NP_001003683			phosphodiesterase 1A isoform 2						activation of phospholipase C activity|nerve growth factor receptor signaling pathway|platelet activation	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			skin(2)|ovary(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.061)															---	---	---	---
PDE1A	5136	broad.mit.edu	37	2	183193223	183193223	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183193223delA	uc002uos.2	-						PDE1A_uc010zfp.1_Intron|PDE1A_uc002uoq.1_Intron|PDE1A_uc010zfq.1_Intron|PDE1A_uc002uor.2_Intron|PDE1A_uc002uov.1_Intron	NM_001003683	NP_001003683			phosphodiesterase 1A isoform 2						activation of phospholipase C activity|nerve growth factor receptor signaling pathway|platelet activation	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			skin(2)|ovary(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.061)															---	---	---	---
PDE1A	5136	broad.mit.edu	37	2	183373160	183373160	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183373160delA	uc002uos.2	-						PDE1A_uc010zfp.1_Intron|PDE1A_uc002uoq.1_Intron|PDE1A_uc010zfq.1_Intron|PDE1A_uc002uov.1_Intron	NM_001003683	NP_001003683			phosphodiesterase 1A isoform 2						activation of phospholipase C activity|nerve growth factor receptor signaling pathway|platelet activation	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			skin(2)|ovary(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.061)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	184074984	184074985	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:184074984_184074985delTT								NUP35 (48577 upstream) : None (None downstream)																																			---	---	---	---
ZNF804A	91752	broad.mit.edu	37	2	185475235	185475235	+	Intron	DEL	T	-	-	rs79414245		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:185475235delT	uc002uph.2	+							NM_194250	NP_919226			zinc finger protein 804A							intracellular	zinc ion binding			ovary(6)|skin(3)|large_intestine(1)|pancreas(1)	11																		---	---	---	---
ZNF804A	91752	broad.mit.edu	37	2	185610454	185610454	+	Intron	DEL	A	-	-	rs72277448		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:185610454delA	uc002uph.2	+							NM_194250	NP_919226			zinc finger protein 804A							intracellular	zinc ion binding			ovary(6)|skin(3)|large_intestine(1)|pancreas(1)	11																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	186052503	186052503	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:186052503delA								ZNF804A (248291 upstream) : None (None downstream)																																			---	---	---	---
FAM171B	165215	broad.mit.edu	37	2	187618916	187618917	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187618916_187618917insT	uc002ups.2	+						FAM171B_uc002upr.1_Intron	NM_177454	NP_803237			KIAA1946							integral to membrane	DNA binding			ovary(6)|breast(3)|central_nervous_system(1)	10																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	187788701	187788704	+	IGR	DEL	AAAC	-	-	rs10562939		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187788701_187788704delAAAC								ZSWIM2 (74804 upstream) : CALCRL (419147 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	187932786	187932786	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187932786delA								ZSWIM2 (218889 upstream) : CALCRL (275065 downstream)																																			---	---	---	---
CALCRL	10203	broad.mit.edu	37	2	188224010	188224010	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:188224010delA	uc002upv.3	-						CALCRL_uc010frt.2_Intron	NM_005795	NP_005786			calcitonin receptor-like precursor							integral to plasma membrane				lung(3)|ovary(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(96;0.227)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	188831933	188831933	+	IGR	DEL	T	-	-	rs77587715		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:188831933delT								TFPI (412714 upstream) : GULP1 (324671 downstream)																																			---	---	---	---
COL3A1	1281	broad.mit.edu	37	2	189850525	189850525	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189850525delA	uc002uqj.1	+							NM_000090	NP_000081			collagen type III alpha 1 preproprotein						axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway	collagen type III|extracellular space	extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding			central_nervous_system(7)|ovary(4)|large_intestine(2)	13			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)|Palifermin(DB00039)													---	---	---	---
COL3A1	1281	broad.mit.edu	37	2	189857867	189857867	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189857867delT	uc002uqj.1	+						COL3A1_uc010frw.1_Intron	NM_000090	NP_000081			collagen type III alpha 1 preproprotein						axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway	collagen type III|extracellular space	extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding			central_nervous_system(7)|ovary(4)|large_intestine(2)	13			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)|Palifermin(DB00039)													---	---	---	---
PMS1	5378	broad.mit.edu	37	2	190717518	190717518	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190717518delA	uc002urh.3	+						PMS1_uc010zga.1_Intron|PMS1_uc010zgb.1_Intron|PMS1_uc002urk.3_Intron|PMS1_uc002uri.3_Intron|PMS1_uc010zgc.1_Intron|PMS1_uc010zgd.1_Intron|PMS1_uc002urj.2_Intron|PMS1_uc010fry.1_Intron|PMS1_uc010frz.2_Intron|PMS1_uc002url.2_Intron|PMS1_uc002urm.2_Intron|PMS1_uc002urn.1_5'Flank	NM_000534	NP_000525			postmeiotic segregation 1 isoform a						mismatch repair|reciprocal meiotic recombination	MutLalpha complex	ATP binding|ATPase activity|mismatched DNA binding			ovary(2)|kidney(1)|central_nervous_system(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0013)|Epithelial(96;0.0263)|all cancers(119;0.0751)					Mis|N			colorectal|endometrial|ovarian		Direct_reversal_of_damage|MMR					---	---	---	---
Unknown	0	broad.mit.edu	37	2	191566996	191566996	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191566996delT								NAB1 (9505 upstream) : GLS (178551 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	191699442	191699445	+	IGR	DEL	TTTA	-	-	rs10535318		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191699442_191699445delTTTA								NAB1 (141951 upstream) : GLS (46102 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	191882666	191882668	+	IGR	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191882666_191882668delTTT								STAT1 (3690 upstream) : STAT4 (11638 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	192793663	192793664	+	IGR	DEL	CA	-	-	rs67177416		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192793663_192793664delCA								SDPR (81682 upstream) : TMEFF2 (21085 downstream)																																			---	---	---	---
TMEFF2	23671	broad.mit.edu	37	2	192866490	192866490	+	Intron	DEL	T	-	-	rs35513403		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192866490delT	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	193077595	193077596	+	IGR	DEL	TT	-	-	rs78149951		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193077595_193077596delTT								TMEFF2 (17951 upstream) : PCGEM1 (536975 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	193642193	193642193	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193642193delA								PCGEM1 (572 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	193820303	193820303	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193820303delT								PCGEM1 (178682 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	193878388	193878388	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193878388delA								PCGEM1 (236767 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	194600551	194600551	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:194600551delA								PCGEM1 (958930 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	195305299	195305300	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:195305299_195305300delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	195866871	195866871	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:195866871delG								None (None upstream) : SLC39A10 (654661 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	196119853	196119853	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196119853delA								None (None upstream) : SLC39A10 (401679 downstream)																																			---	---	---	---
DNAH7	56171	broad.mit.edu	37	2	196722321	196722321	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196722321delT	uc002utj.3	-	44	8295	c.8194delA	c.(8194-8196)ATTfs	p.I2732fs		NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	2732	Stalk (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12																		---	---	---	---
DNAH7	56171	broad.mit.edu	37	2	196862401	196862401	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196862401delA	uc002utj.3	-							NM_018897	NP_061720			dynein, axonemal, heavy chain 7						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12																		---	---	---	---
CCDC150	284992	broad.mit.edu	37	2	197550340	197550341	+	Intron	DEL	TT	-	-	rs71886351		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197550340_197550341delTT	uc002utp.1	+						CCDC150_uc010zgq.1_Intron|CCDC150_uc010zgr.1_Intron|CCDC150_uc010zgs.1_Intron	NM_001080539	NP_001074008			coiled-coil domain containing 150												0																		---	---	---	---
C2orf66	401027	broad.mit.edu	37	2	197674461	197674461	+	5'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197674461delA	uc002utv.2	-	1						NM_213608	NP_998773			hypothetical protein LOC401027 precursor							extracellular region					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	197805623	197805624	+	IGR	DEL	CA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197805623_197805624delCA								PGAP1 (13104 upstream) : ANKRD44 (26119 downstream)																																			---	---	---	---
ANKRD44	91526	broad.mit.edu	37	2	197866697	197866699	+	Intron	DEL	AAT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197866697_197866699delAAT	uc002uua.1	-						ANKRD44_uc002utz.3_Intron	NM_153697	NP_710181			ankyrin repeat domain 44								protein binding			ovary(4)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.246)															---	---	---	---
ANKRD44	91526	broad.mit.edu	37	2	197888297	197888297	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197888297delA	uc002uua.1	-						ANKRD44_uc002utz.3_Intron	NM_153697	NP_710181			ankyrin repeat domain 44								protein binding			ovary(4)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.246)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	199641593	199641593	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:199641593delT								PLCL1 (626987 upstream) : SATB2 (492631 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	200561359	200561360	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200561359_200561360delAA								FLJ32063 (219701 upstream) : C2orf69 (214619 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	200885952	200885953	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200885952_200885953delTG								C2orf47 (57107 upstream) : SPATS2L (284651 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	201043520	201043520	+	IGR	DEL	A	-	-	rs35608644		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201043520delA								C2orf47 (214675 upstream) : SPATS2L (127084 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	201603017	201603019	+	IGR	DEL	AAA	-	-	rs113018766		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201603017_201603019delAAA								AOX1 (66802 upstream) : AOX2P (32376 downstream)																																			---	---	---	---
BZW1	9689	broad.mit.edu	37	2	201686851	201686851	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201686851delT	uc010zhg.1	+						BZW1_uc002uwc.2_Intron	NM_014670	NP_055485			basic leucine zipper and W2 domains 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm	protein binding				0																		---	---	---	---
CLK1	1195	broad.mit.edu	37	2	201719893	201719893	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201719893delA	uc002uwe.2	-						CLK1_uc002uwd.2_Intron|CLK1_uc010zhi.1_Intron|CLK1_uc002uwf.2_Intron|CLK1_uc002uwg.2_Intron|CLK1_uc010fsv.2_Intron	NM_004071	NP_004062			CDC-like kinase 1 isoform 1						cell proliferation	nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein serine/threonine kinase activity			pancreas(2)	2																		---	---	---	---
FAM126B	285172	broad.mit.edu	37	2	201933740	201933740	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201933740delA	uc002uws.3	-						FAM126B_uc002uwu.2_Intron|FAM126B_uc002uwv.2_Intron|FAM126B_uc002uww.1_Intron|NDUFB3_uc002uwx.3_5'Flank	NM_173822	NP_776183			hypothetical protein LOC285172							intracellular				ovary(1)	1																		---	---	---	---
CASP8	841	broad.mit.edu	37	2	202137289	202137289	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202137289delA	uc002uxr.1	+						CASP8_uc010ftc.1_Intron|CASP8_uc002uxo.1_Intron|CASP8_uc002uxp.1_Intron|CASP8_uc002uxq.1_Intron|CASP8_uc002uxs.1_Intron|CASP8_uc002uxt.1_Intron|CASP8_uc002uxu.1_Intron|CASP8_uc010ftd.1_Intron|CASP8_uc002uxv.1_Intron|CASP8_uc002uxw.1_Intron|CASP8_uc002uxy.1_Intron|CASP8_uc002uxx.1_Intron|CASP8_uc010ftf.2_Intron|CASP8_uc010fte.1_Intron	NM_033355	NP_203519			caspase 8 isoform B precursor						activation of caspase activity|activation of pro-apoptotic gene products|cellular component disassembly involved in apoptosis|cellular response to mechanical stimulus|induction of apoptosis by extracellular signals|induction of apoptosis by intracellular signals|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis involved in cellular protein catabolic process|response to tumor necrosis factor	centrosome|cytosol|mitochondrial outer membrane	cysteine-type endopeptidase activity|protein binding|protein binding			upper_aerodigestive_tract(2)|ovary(1)|breast(1)|skin(1)	5															HNSCC(4;0.00038)			---	---	---	---
ALS2CR11	151254	broad.mit.edu	37	2	202439773	202439774	+	Intron	INS	-	G	G	rs13394004		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202439773_202439774insG	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																		---	---	---	---
ALS2	57679	broad.mit.edu	37	2	202639470	202639470	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202639470delT	uc002uyo.2	-						ALS2_uc002uyp.3_Intron|ALS2_uc002uyq.2_Intron|ALS2_uc002uyr.2_Intron	NM_020919	NP_065970			alsin isoform 1						cell death|endosome organization|positive regulation of Rac GTPase activity|regulation of endosome size	centrosome|cytosol|early endosome|growth cone|lamellipodium|protein complex|ruffle	protein homodimerization activity|protein serine/threonine kinase activator activity|Rab GTPase binding|Rab guanyl-nucleotide exchange factor activity|Rac guanyl-nucleotide exchange factor activity|Ran guanyl-nucleotide exchange factor activity			skin(5)|lung(1)|breast(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	202988575	202988576	+	Intron	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202988575_202988576delTC	uc010zhu.1	+											SubName: Full=cDNA FLJ52575;																														---	---	---	---
BMPR2	659	broad.mit.edu	37	2	203387552	203387552	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203387552delA	uc002uzf.3	+						BMPR2_uc010ftr.2_Intron	NM_001204	NP_001195			bone morphogenetic protein receptor type II						anterior/posterior pattern formation|BMP signaling pathway|cellular response to starvation|lung alveolus development|mesoderm formation|negative regulation of cell growth|negative regulation of systemic arterial blood pressure|negative regulation of vasoconstriction|positive regulation of BMP signaling pathway|positive regulation of bone mineralization|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of epithelial cell migration|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|regulation of lung blood pressure|transcription from RNA polymerase II promoter|vascular endothelial growth factor receptor signaling pathway	integral to plasma membrane	ATP binding|metal ion binding|transforming growth factor beta receptor activity			ovary(4)|breast(2)|large_intestine(1)|stomach(1)|pancreas(1)	9																		---	---	---	---
BMPR2	659	broad.mit.edu	37	2	203416425	203416425	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203416425delT	uc002uzf.3	+						BMPR2_uc010ftr.2_Intron	NM_001204	NP_001195			bone morphogenetic protein receptor type II						anterior/posterior pattern formation|BMP signaling pathway|cellular response to starvation|lung alveolus development|mesoderm formation|negative regulation of cell growth|negative regulation of systemic arterial blood pressure|negative regulation of vasoconstriction|positive regulation of BMP signaling pathway|positive regulation of bone mineralization|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of epithelial cell migration|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|regulation of lung blood pressure|transcription from RNA polymerase II promoter|vascular endothelial growth factor receptor signaling pathway	integral to plasma membrane	ATP binding|metal ion binding|transforming growth factor beta receptor activity			ovary(4)|breast(2)|large_intestine(1)|stomach(1)|pancreas(1)	9																		---	---	---	---
WDR12	55759	broad.mit.edu	37	2	203764221	203764221	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203764221delA	uc002uzl.2	-						WDR12_uc010ftt.2_Intron	NM_018256	NP_060726			WD repeat domain 12 protein						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																		---	---	---	---
ALS2CR8	79800	broad.mit.edu	37	2	203807442	203807442	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203807442delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	203868163	203868163	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203868163delT								ALS2CR8 (17103 upstream) : NBEAL1 (11439 downstream)																																			---	---	---	---
CYP20A1	57404	broad.mit.edu	37	2	204110555	204110555	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204110555delT	uc002uzv.3	+						CYP20A1_uc002uzx.3_Intron|CYP20A1_uc010zif.1_Intron|CYP20A1_uc002uzy.3_Intron|CYP20A1_uc002uzw.3_Intron	NM_177538	NP_803882			cytochrome P450, family 20, subfamily A,							integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen				0																		---	---	---	---
ABI2	10152	broad.mit.edu	37	2	204265919	204265919	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204265919delT	uc002vaa.2	+						ABI2_uc002uzz.2_Intron|ABI2_uc010zih.1_Intron|ABI2_uc010zii.1_Intron|ABI2_uc010zij.1_Intron|ABI2_uc002vab.2_Intron|ABI2_uc010zik.1_Intron|ABI2_uc010zil.1_Intron|ABI2_uc010zim.1_Intron|ABI2_uc002vac.2_Intron|ABI2_uc010zin.1_Intron	NM_005759	NP_005750			abl interactor 2						actin polymerization or depolymerization|cell migration|peptidyl-tyrosine phosphorylation	cytoskeleton|cytosol|filopodium|lamellipodium	cytoskeletal adaptor activity|DNA binding|kinase binding|proline-rich region binding|SH3 domain binding|ubiquitin protein ligase binding				0																		---	---	---	---
CD28	940	broad.mit.edu	37	2	204578612	204578613	+	Intron	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204578612_204578613delGT	uc002vah.3	+						CD28_uc002vag.1_Intron|CD28_uc010zio.1_Intron|CD28_uc010ftx.2_Intron|CD28_uc002vaj.3_Intron	NM_006139	NP_006130			CD28 antigen precursor						cell surface receptor linked signaling pathway|cytokine biosynthetic process|humoral immune response|positive regulation of anti-apoptosis|positive regulation of interleukin-2 biosynthetic process|positive regulation of mitosis|positive regulation of translation|positive regulation of viral genome replication|regulation of defense response to virus by virus|regulatory T cell differentiation|T cell costimulation|viral reproduction	cytosol|external side of plasma membrane|integral to plasma membrane	coreceptor activity|protease binding|SH3/SH2 adaptor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	205379641	205379641	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205379641delA								ICOS (553345 upstream) : PARD3B (30875 downstream)																																			---	---	---	---
PARD3B	117583	broad.mit.edu	37	2	205455564	205455564	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205455564delA	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	205920932	205920932	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205920932delT	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	206161998	206161998	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206161998delA	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	206980715	206980715	+	RNA	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206980715delT	uc002vbc.1	-	1		c.1574delA								Homo sapiens cDNA FLJ35491 fis, clone SMINT2008625, moderately similar to GLYCINE CLEAVAGE SYSTEM H PROTEIN PRECURSOR.																														---	---	---	---
DYTN	391475	broad.mit.edu	37	2	207542714	207542714	+	Intron	DEL	A	-	-	rs66801707		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207542714delA	uc002vbr.1	-							NM_001093730	NP_001087199			dystrotelin							plasma membrane	zinc ion binding			ovary(1)|central_nervous_system(1)	2				LUSC - Lung squamous cell carcinoma(261;0.082)|Epithelial(149;0.129)|Lung(261;0.153)														---	---	---	---
CREB1	1385	broad.mit.edu	37	2	208407945	208407945	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208407945delT	uc002vcc.2	+						CREB1_uc010ziz.1_Intron|CREB1_uc002vcd.2_Intron	NM_134442	NP_604391			cAMP responsive element binding protein 1						activation of phospholipase C activity|axon guidance|innate immune response|interspecies interaction between organisms|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|protein phosphorylation|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway		protein dimerization activity|transcription cofactor activity		EWSR1/CREB1(42)	soft_tissue(42)|breast(1)|central_nervous_system(1)	44				LUSC - Lung squamous cell carcinoma(261;0.0768)|Epithelial(149;0.127)|Lung(261;0.145)	Adenosine monophosphate(DB00131)|Bromocriptine(DB01200)|Naloxone(DB01183)			T	EWSR1	clear cell sarcoma|angiomatoid fibrous histiocytoma								---	---	---	---
Unknown	0	broad.mit.edu	37	2	208502289	208502290	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208502289_208502290delTT								FAM119A (12224 upstream) : CCNYL1 (73974 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	208550874	208550874	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208550874delA								FAM119A (60809 upstream) : CCNYL1 (25390 downstream)																																			---	---	---	---
PLEKHM3	389072	broad.mit.edu	37	2	208715458	208715458	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208715458delA	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	208921915	208921915	+	IGR	DEL	T	-	-	rs74577733	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208921915delT								PLEKHM3 (31631 upstream) : CRYGD (64417 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	208956513	208956513	+	IGR	DEL	T	-	-	rs76479194		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208956513delT								PLEKHM3 (66229 upstream) : CRYGD (29819 downstream)																																			---	---	---	---
PTH2R	5746	broad.mit.edu	37	2	209279629	209279629	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209279629delA	uc002vdb.2	+						PTH2R_uc010zjb.1_Intron	NM_005048	NP_005039			parathyroid hormone 2 receptor precursor							integral to plasma membrane	parathyroid hormone receptor activity			ovary(1)|breast(1)|skin(1)	3				Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)														---	---	---	---
PTH2R	5746	broad.mit.edu	37	2	209455332	209455333	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209455332_209455333delTT	uc010fuo.1	+											Homo sapiens cDNA FLJ60238 complete cds, highly similar to Parathyroid hormone receptor precursor.							integral to plasma membrane	parathyroid hormone receptor activity			ovary(1)|breast(1)|skin(1)	3				Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	209853792	209853792	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209853792delT								PTH2R (148974 upstream) : MAP2 (434979 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	209945671	209945671	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209945671delC								PTH2R (240853 upstream) : MAP2 (343100 downstream)																																			---	---	---	---
MAP2	4133	broad.mit.edu	37	2	210288885	210288885	+	5'UTR	DEL	C	-	-	rs113563544		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210288885delC	uc002vdc.1	+	1					MAP2_uc002vdd.1_5'UTR	NM_002374	NP_002365			microtubule-associated protein 2 isoform 1						central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity			ovary(9)|upper_aerodigestive_tract(2)|large_intestine(2)|pancreas(2)|central_nervous_system(1)|skin(1)	17		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Estramustine(DB01196)													---	---	---	---
MYL1	4632	broad.mit.edu	37	2	211158848	211158848	+	Intron	DEL	T	-	-	rs13427549	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211158848delT	uc002vec.2	-						MYL1_uc002veb.2_Intron	NM_079420	NP_524144			fast skeletal myosin alkali light chain 1						muscle filament sliding|muscle organ development	cytosol|muscle myosin complex|sarcomere	calcium ion binding|structural constituent of muscle			ovary(1)	1				Epithelial(149;0.00573)|Lung(261;0.0422)|LUSC - Lung squamous cell carcinoma(261;0.0444)|all cancers(144;0.057)														---	---	---	---
ERBB4	2066	broad.mit.edu	37	2	212474576	212474576	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212474576delA	uc002veg.1	-						ERBB4_uc002veh.1_Intron|ERBB4_uc010zji.1_Intron|ERBB4_uc010zjj.1_Intron|ERBB4_uc010fut.1_Intron	NM_005235	NP_005226			v-erb-a erythroblastic leukemia viral oncogene						cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transmembrane receptor protein tyrosine kinase signaling pathway	basolateral plasma membrane|cytoplasm|integral to membrane|nucleus	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(21)|skin(5)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	33		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)											TSP Lung(8;0.080)			---	---	---	---
ERBB4	2066	broad.mit.edu	37	2	212717967	212717967	+	Intron	DEL	T	-	-	rs72115061		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212717967delT	uc002veg.1	-						ERBB4_uc002veh.1_Intron|ERBB4_uc010zji.1_Intron|ERBB4_uc010zjj.1_Intron|ERBB4_uc010fut.1_Intron	NM_005235	NP_005226			v-erb-a erythroblastic leukemia viral oncogene						cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transmembrane receptor protein tyrosine kinase signaling pathway	basolateral plasma membrane|cytoplasm|integral to membrane|nucleus	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(21)|skin(5)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	33		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)											TSP Lung(8;0.080)			---	---	---	---
IKZF2	22807	broad.mit.edu	37	2	213880502	213880502	+	Intron	DEL	A	-	-	rs78983185		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:213880502delA	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|IKZF2_uc002vei.2_5'Flank	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	214367016	214367016	+	Intron	DEL	T	-	-	rs115962591	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214367016delT	uc002veq.2	+						SPAG16_uc010fuz.1_Intron|SPAG16_uc002ver.2_Intron|SPAG16_uc010zjk.1_Intron	NM_024532	NP_078808			sperm associated antigen 16 isoform 1						cilium assembly	cilium axoneme|flagellar axoneme				ovary(1)|skin(1)	2		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	216352704	216352706	+	IGR	DEL	TAT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216352704_216352706delTAT								FN1 (51913 upstream) : MREG (454609 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	216480470	216480470	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216480470delA	uc002vfm.1	-											Homo sapiens cDNA FLJ34546 fis, clone HLUNG2008959.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	216786357	216786357	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216786357delT								FN1 (485566 upstream) : MREG (20958 downstream)																																			---	---	---	---
MREG	55686	broad.mit.edu	37	2	216810961	216810963	+	Intron	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216810961_216810963delAAA	uc002vfo.2	-						MREG_uc002vfq.2_Intron	NM_018000	NP_060470			whn-dependent transcript 2							apical plasma membrane					0		Renal(323;0.0328)		Epithelial(149;4.64e-07)|all cancers(144;5.56e-05)|LUSC - Lung squamous cell carcinoma(224;0.00832)|Lung(261;0.0111)														---	---	---	---
MARCH4	57574	broad.mit.edu	37	2	217232173	217232173	+	Intron	DEL	A	-	-	rs111286697		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217232173delA	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	218537757	218537757	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218537757delA	uc002vgo.2	-							NR_026597				Homo sapiens cDNA FLJ14199 fis, clone NT2RP3002713.												0																		---	---	---	---
DIRC3	729582	broad.mit.edu	37	2	218537764	218537765	+	Intron	INS	-	G	G	rs145256552	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218537764_218537765insG	uc002vgo.2	-							NR_026597				Homo sapiens cDNA FLJ14199 fis, clone NT2RP3002713.												0																		---	---	---	---
TNS1	7145	broad.mit.edu	37	2	218695642	218695642	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218695642delG	uc002vgt.2	-						TNS1_uc002vgr.2_Intron|TNS1_uc002vgs.2_Intron|TNS1_uc010zjv.1_Intron	NM_022648	NP_072174			tensin							cytoplasm|cytoskeleton|focal adhesion	actin binding			ovary(3)|breast(1)	4		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)														---	---	---	---
RUFY4	285180	broad.mit.edu	37	2	218942092	218942093	+	Intron	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218942092_218942093delTC	uc002vgw.2	+						RUFY4_uc002vgy.1_Intron|RUFY4_uc010fvl.1_Intron	NM_198483	NP_940885			RUN and FYVE domain containing 4								metal ion binding			pancreas(1)	1		Renal(207;0.0915)		Epithelial(149;4.11e-06)|all cancers(144;0.000519)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)														---	---	---	---
CXCR2	3579	broad.mit.edu	37	2	218987576	218987576	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218987576delT	uc002vgz.1	+							NM_001557	NP_001548			interleukin 8 receptor beta						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|cellular defense response|dendritic cell chemotaxis|inflammatory response|neutrophil activation|neutrophil chemotaxis|positive regulation of cell proliferation	cell surface|integral to plasma membrane|mast cell granule	interleukin-8 receptor activity			lung(1)|breast(1)	2																		---	---	---	---
C2orf62	375307	broad.mit.edu	37	2	219225180	219225180	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219225180delT	uc002vhr.2	+						C2orf62_uc002vhs.2_Intron	NM_198559	NP_940961			hypothetical protein LOC375307												0		Renal(207;0.0915)		Epithelial(149;8.08e-07)|all cancers(144;0.000146)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
USP37	57695	broad.mit.edu	37	2	219330590	219330590	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219330590delT	uc002vie.2	-						USP37_uc010fvs.1_Intron|USP37_uc010zkf.1_Intron|USP37_uc002vif.2_Intron|USP37_uc002vig.2_Intron	NM_020935	NP_065986			ubiquitin specific peptidase 37						ubiquitin-dependent protein catabolic process	nucleus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			skin(3)|ovary(1)|prostate(1)	5		Renal(207;0.0915)		Epithelial(149;1.08e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.00375)|Lung(261;0.00487)														---	---	---	---
PLCD4	84812	broad.mit.edu	37	2	219472042	219472042	+	5'Flank	DEL	A	-	-	rs113680171		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219472042delA	uc002vij.1	+						PLCD4_uc010zkj.1_5'Flank	NM_032726	NP_116115			phospholipase C, delta 4						intracellular signal transduction|lipid catabolic process	endoplasmic reticulum|membrane|nucleus	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(3)	3		Renal(207;0.0915)		Epithelial(149;5.11e-07)|all cancers(144;0.000104)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	219681915	219681916	+	5'Flank	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219681915_219681916delAA	uc002vja.1	+											Homo sapiens cDNA FLJ36538 fis, clone TRACH2005159.																														---	---	---	---
OBSL1	23363	broad.mit.edu	37	2	220418280	220418280	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220418280delG	uc010fwk.2	-							NM_015311	NP_056126			obscurin-like 1						cardiac myofibril assembly	intercalated disc|M band|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity				0		Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	220901599	220901599	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220901599delA								SLC4A3 (394898 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	222030993	222030994	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222030993_222030994delTT								None (None upstream) : EPHA4 (251755 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	222046648	222046648	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222046648delT								None (None upstream) : EPHA4 (236101 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	222146281	222146281	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222146281delT								None (None upstream) : EPHA4 (136468 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	222754619	222754620	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222754619_222754620delAA								EPHA4 (315697 upstream) : PAX3 (309987 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	222768767	222768767	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222768767delA								EPHA4 (329845 upstream) : PAX3 (295840 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	223956172	223956172	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223956172delT								KCNE4 (35819 upstream) : SCG2 (505488 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	224442874	224442874	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224442874delA								KCNE4 (522521 upstream) : SCG2 (18786 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	224490886	224490888	+	IGR	DEL	AGG	-	-	rs62190118	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224490886_224490888delAGG								SCG2 (23765 upstream) : AP1S3 (129160 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	225064335	225064335	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225064335delA								SERPINE2 (160299 upstream) : FAM124B (179081 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	225572690	225572701	+	IGR	DEL	TCCCTCCCTCCC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225572690_225572701delTCCCTCCCTCCC								CUL3 (122580 upstream) : DOCK10 (57106 downstream)																																			---	---	---	---
DOCK10	55619	broad.mit.edu	37	2	225698204	225698204	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225698204delT	uc010fwz.1	-						DOCK10_uc002vob.2_Intron	NM_014689	NP_055504			dedicator of cytokinesis 10								GTP binding			ovary(2)	2		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	227864003	227864003	+	IGR	DEL	T	-	-	rs79253548		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227864003delT								RHBDD1 (2412 upstream) : COL4A4 (3432 downstream)																																			---	---	---	---
COL4A4	1286	broad.mit.edu	37	2	227964172	227964172	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227964172delA	uc010zlt.1	-							NM_000092	NP_000083			alpha 4 type IV collagen precursor						axon guidance|glomerular basement membrane development	basal lamina|collagen type IV	extracellular matrix structural constituent|protein binding			ovary(5)|central_nervous_system(3)|pancreas(1)|breast(1)|skin(1)	11		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)														---	---	---	---
COL4A3	1285	broad.mit.edu	37	2	228118619	228118619	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228118619delA	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	228642529	228642532	+	IGR	DEL	TCCT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228642529_228642532delTCCT								SLC19A3 (59784 upstream) : CCL20 (36026 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	229587657	229587657	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229587657delA								SPHKAP (541296 upstream) : PID1 (301033 downstream)																																			---	---	---	---
PID1	55022	broad.mit.edu	37	2	230022671	230022672	+	Intron	INS	-	T	T	rs144472560	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230022671_230022672insT	uc002vpr.3	-						PID1_uc002vps.3_Intron|PID1_uc002vpt.3_Intron|PID1_uc002vpu.3_Intron	NM_001100818	NP_001094288			phosphotyrosine interaction domain containing 1							cytoplasm				breast(3)|skin(1)	4		Renal(207;0.0112)|all_lung(227;0.0191)|Lung NSC(271;0.0851)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.171)		Epithelial(121;3.08e-11)|all cancers(144;2.28e-08)|LUSC - Lung squamous cell carcinoma(224;0.0145)|Lung(261;0.0189)														---	---	---	---
DNER	92737	broad.mit.edu	37	2	230422453	230422454	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230422453_230422454delAA	uc002vpv.2	-						DNER_uc010zly.1_Intron	NM_139072	NP_620711			delta-notch-like EGF repeat-containing						central nervous system development|endocytosis|neuron migration|Notch signaling pathway|synapse assembly	dendrite|early endosome|integral to membrane|plasma membrane	calcium ion binding|clathrin binding|transmembrane receptor activity			lung(5)|ovary(2)|skin(1)	8		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)														---	---	---	---
SP140L	93349	broad.mit.edu	37	2	231267926	231267926	+	3'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231267926delT	uc010fxm.1	+	19						NM_138402	NP_612411			SP140 nuclear body protein-like							nucleus	DNA binding|metal ion binding			central_nervous_system(1)	1																		---	---	---	---
SP100	6672	broad.mit.edu	37	2	231316896	231316897	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231316896_231316897delTT	uc002vqt.2	+						SP100_uc002vqs.2_Intron|SP100_uc002vqu.1_Intron|SP100_uc010zmb.1_Intron|SP100_uc002vqq.1_Intron|SP100_uc002vqr.1_Intron|SP100_uc010zmc.1_Intron|SP100_uc002vqv.1_Intron	NM_003113	NP_003104			nuclear antigen Sp100 isoform 2						DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|interspecies interaction between organisms|negative regulation of cellular component movement|negative regulation of DNA binding|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|negative regulation of transcription, DNA-dependent|negative regulation of viral transcription|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|response to cytokine stimulus|response to retinoic acid|response to type I interferon	cytoplasm|nuclear periphery|nucleolus|PML body	chromo shadow domain binding|DNA binding|identical protein binding|kinase binding|protein homodimerization activity|transcription coactivator activity|transcription corepressor activity|transcription factor binding			ovary(4)|central_nervous_system(1)	5		Renal(207;0.0112)|all_lung(227;0.0335)|all_hematologic(139;0.0749)|Lung NSC(271;0.142)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	231559678	231559679	+	RNA	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231559678_231559679insA	uc002vqw.1	-	3		c.883_884insT								Homo sapiens cDNA FLJ30454 fis, clone BRACE2009311.																														---	---	---	---
CAB39	51719	broad.mit.edu	37	2	231616963	231616964	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231616963_231616964delAA	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)														---	---	---	---
SPATA3	130560	broad.mit.edu	37	2	231870053	231870055	+	Intron	DEL	CAC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231870053_231870055delCAC	uc010zmd.1	+						SPATA3_uc002vri.3_Intron|SPATA3_uc002vrk.2_Intron	NM_139073	NP_620712			testis and spermatogenesis cell apoptosis						apoptosis|spermatogenesis						0																		---	---	---	---
ARMC9	80210	broad.mit.edu	37	2	232115358	232115358	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232115358delG	uc002vrq.3	+						ARMC9_uc002vrp.3_Intron	NM_025139	NP_079415			armadillo repeat containing 9								binding			ovary(1)	1		Renal(207;0.0112)|all_lung(227;0.0744)|all_hematologic(139;0.0749)|Acute lymphoblastic leukemia(138;0.167)|Medulloblastoma(418;0.184)|Lung NSC(271;0.205)		Epithelial(121;1.43e-10)|LUSC - Lung squamous cell carcinoma(224;0.017)|Lung(119;0.0189)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	232298590	232298590	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232298590delA								B3GNT7 (32717 upstream) : NCL (20870 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	233456161	233456163	+	IGR	DEL	AAG	-	-	rs148692012	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233456161_233456163delAAG								EIF4E2 (7812 upstream) : EFHD1 (14604 downstream)																																			---	---	---	---
GIGYF2	26058	broad.mit.edu	37	2	233639775	233639776	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233639775_233639776delTT	uc002vti.3	+						GIGYF2_uc010zmj.1_Intron|GIGYF2_uc002vtg.2_Intron|GIGYF2_uc002vtj.3_Intron|GIGYF2_uc002vtk.3_Intron|GIGYF2_uc002vth.3_Intron|GIGYF2_uc010zmk.1_Intron|GIGYF2_uc010zml.1_Intron|KCNJ13_uc002vtp.2_Intron	NM_015575	NP_056390			GRB10 interacting GYF protein 2 isoform b						cell death		protein binding			ovary(4)|central_nervous_system(3)	7		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)														---	---	---	---
GIGYF2	26058	broad.mit.edu	37	2	233641825	233641826	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233641825_233641826delTT	uc002vti.3	+						GIGYF2_uc010zmj.1_Intron|GIGYF2_uc002vtg.2_Intron|GIGYF2_uc002vtj.3_Intron|GIGYF2_uc002vtk.3_Intron|GIGYF2_uc002vth.3_Intron|GIGYF2_uc010zmk.1_Intron|GIGYF2_uc010zml.1_Intron|KCNJ13_uc002vtp.2_5'Flank	NM_015575	NP_056390			GRB10 interacting GYF protein 2 isoform b						cell death		protein binding			ovary(4)|central_nervous_system(3)	7		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)														---	---	---	---
NGEF	25791	broad.mit.edu	37	2	233814193	233814194	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233814193_233814194delTT	uc002vts.2	-							NM_019850	NP_062824			neuronal guanine nucleotide exchange factor						apoptosis|cell differentiation|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|growth cone|plasma membrane	Rho guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)|skin(1)	7		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.00793)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;8.65e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(119;0.00984)|GBM - Glioblastoma multiforme(43;0.0604)														---	---	---	---
INPP5D	3635	broad.mit.edu	37	2	234061510	234061510	+	Intron	DEL	G	-	-	rs36172029		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234061510delG	uc010zmo.1	+						INPP5D_uc010zmp.1_Intron	NM_001017915	NP_001017915			SH2 containing inositol phosphatase isoform a						apoptosis|blood coagulation|leukocyte migration|T cell receptor signaling pathway	cytosol	inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|SH3 domain binding			ovary(1)|central_nervous_system(1)	2		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843)		Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	234258547	234258547	+	IGR	DEL	T	-	-	rs34530137		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234258547delT								SAG (2846 upstream) : DGKD (4606 downstream)																																			---	---	---	---
HJURP	55355	broad.mit.edu	37	2	234761358	234761358	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234761358delA	uc002vvg.2	-						HJURP_uc010znd.1_Intron|HJURP_uc010zne.1_Intron	NM_018410	NP_060880			Holliday junction recognition protein						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	234787921	234787921	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234787921delT								MSL3L2 (10866 upstream) : TRPM8 (38122 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	235235481	235235481	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235235481delT								SPP2 (249705 upstream) : ARL4C (166207 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	235307604	235307604	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235307604delG								SPP2 (321828 upstream) : ARL4C (94084 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	235999670	235999673	+	IGR	DEL	TCTT	-	-	rs34790552		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235999670_235999673delTCTT								SH3BP4 (35314 upstream) : AGAP1 (403063 downstream)																																			---	---	---	---
AGAP1	116987	broad.mit.edu	37	2	236626781	236626782	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236626781_236626782delTT	uc002vvs.2	+						AGAP1_uc002vvt.2_Intron	NM_001037131	NP_001032208			centaurin, gamma 2 isoform 1						protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
AGAP1	116987	broad.mit.edu	37	2	236845579	236845579	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236845579delT	uc002vvs.2	+						AGAP1_uc002vvt.2_Intron	NM_001037131	NP_001032208			centaurin, gamma 2 isoform 1						protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	237423516	237423516	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237423516delG								IQCA1 (7424 upstream) : CXCR7 (45908 downstream)																																			---	---	---	---
LRRFIP1	9208	broad.mit.edu	37	2	238658935	238658935	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238658935delT	uc002vxe.2	+						LRRFIP1_uc002vxc.2_Intron|LRRFIP1_uc010znm.1_Intron|LRRFIP1_uc002vxd.2_Intron|LRRFIP1_uc002vxf.2_Intron	NM_001137552	NP_001131024			leucine rich repeat (in FLII) interacting						negative regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|cytoskeleton|nucleus	DNA binding|double-stranded RNA binding|protein binding			breast(3)	3		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	238843995	238843996	+	IGR	DEL	AA	-	-	rs72483587		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238843995_238843996delAA								RAMP1 (23242 upstream) : UBE2F (31704 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	239313335	239313335	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239313335delG								TRAF3IP1 (3796 upstream) : ASB1 (22291 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	239376852	239376852	+	IGR	DEL	T	-	-	rs68187967		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239376852delT								ASB1 (15962 upstream) : TWIST2 (379821 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	239692159	239692159	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239692159delC								ASB1 (331269 upstream) : TWIST2 (64514 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	239938927	239938928	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239938927_239938928delTG								TWIST2 (106690 upstream) : HDAC4 (30937 downstream)																																			---	---	---	---
HDAC4	9759	broad.mit.edu	37	2	240014546	240014546	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240014546delT	uc002vyk.3	-						HDAC4_uc010fyz.1_Intron|HDAC4_uc010fyy.2_Intron	NM_006037	NP_006028			histone deacetylase 4						B cell differentiation|cardiac muscle hypertrophy in response to stress|chromatin remodeling|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of glycolysis|negative regulation of myotube differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nervous system development|peptidyl-lysine deacetylation|positive regulation of cell proliferation|positive regulation of protein sumoylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|response to denervation involved in regulation of muscle adaptation|response to interleukin-1|transcription, DNA-dependent	histone deacetylase complex|transcriptional repressor complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|potassium ion binding|repressing transcription factor binding|zinc ion binding			breast(3)|skin(2)|ovary(1)	6		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)														---	---	---	---
HDAC4	9759	broad.mit.edu	37	2	240225382	240225382	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240225382delT	uc002vyk.3	-						HDAC4_uc010fza.2_Intron|hsa-mir-4269|MI0015875_5'Flank	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	240338015	240338015	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240338015delA								HDAC4 (14669 upstream) : NDUFA10 (562143 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	240349528	240349528	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240349528delT								HDAC4 (26182 upstream) : NDUFA10 (550630 downstream)																																			---	---	---	---
NDUFA10	4705	broad.mit.edu	37	2	240951506	240951508	+	Intron	DEL	TCT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240951506_240951508delTCT	uc002vyn.2	-						NDUFA10_uc010fzc.1_Intron|NDUFA10_uc002vyo.1_3'UTR	NM_004544	NP_004535			NADH dehydrogenase (ubiquinone) 1 alpha						mitochondrial electron transport, NADH to ubiquinone|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|transport	mitochondrial matrix|mitochondrial respiratory chain complex I	ATP binding|NADH dehydrogenase (ubiquinone) activity|phosphotransferase activity, alcohol group as acceptor			central_nervous_system(1)	1		all_epithelial(40;4.26e-15)|Breast(86;4.4e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0396)|Lung NSC(271;0.128)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(121;7.82e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.5e-13)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;2.39e-05)|Lung(119;0.00519)|LUSC - Lung squamous cell carcinoma(224;0.0202)	NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	241171248	241171248	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241171248delA								OTOS (91175 upstream) : GPC1 (203867 downstream)																																			---	---	---	---
SNED1	25992	broad.mit.edu	37	2	241944306	241944306	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241944306delT	uc002wah.1	+							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)														---	---	---	---
SNED1	25992	broad.mit.edu	37	2	242021000	242021001	+	Intron	INS	-	TCAGG	TCAGG	rs140631844	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242021000_242021001insTCAGG	uc002wah.1	+						SNED1_uc002wai.1_Intron|SNED1_uc002waj.1_Intron	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)														---	---	---	---
STK25	10494	broad.mit.edu	37	2	242441854	242441854	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242441854delA	uc002wbm.2	-						STK25_uc002wbk.2_5'Flank|STK25_uc002wbl.2_5'Flank|STK25_uc002wbn.2_Intron|STK25_uc002wbo.2_Intron|STK25_uc010zos.1_Intron|STK25_uc010zot.1_Intron|STK25_uc002wbp.2_Intron|STK25_uc010fzo.2_Intron|STK25_uc010zou.1_Intron|STK25_uc010zov.1_Intron|STK25_uc010zow.1_Intron	NM_006374	NP_006365			serine/threonine kinase 25						response to oxidative stress|signal transduction	Golgi apparatus	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity				0		all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2)		Epithelial(32;8.24e-34)|all cancers(36;3.46e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.6e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.1e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0839)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	242488877	242488877	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242488877delA								STK25 (39917 upstream) : BOK (9315 downstream)																																			---	---	---	---
THAP4	51078	broad.mit.edu	37	2	242561357	242561357	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242561357delA	uc002wbt.2	-							NM_015963	NP_057047			THAP domain containing 4 isoform 1								DNA binding|metal ion binding				0		all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2)		Epithelial(32;2.3e-33)|all cancers(36;8.99e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.68e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0844)														---	---	---	---
ATG4B	23192	broad.mit.edu	37	2	242608184	242608184	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242608184delT	uc002wbv.2	+						ATG4B_uc002wbu.2_Intron|ATG4B_uc002wbw.2_Intron|ATG4B_uc010zox.1_Intron|ATG4B_uc010zoy.1_Intron|ATG4B_uc010fzp.2_Intron|ATG4B_uc010zoz.1_Intron|ATG4B_uc002wby.2_Intron	NM_013325	NP_037457			APG4 autophagy 4 homolog B isoform a						autophagic vacuole assembly|protein transport|proteolysis	cytoplasm	cysteine-type peptidase activity|protein binding				0		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;2.44e-33)|all cancers(36;5.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.75e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0848)														---	---	---	---
CHL1	10752	broad.mit.edu	37	3	424418	424418	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:424418delA	uc003bou.2	+						CHL1_uc003bot.2_Intron|CHL1_uc003bow.1_Intron|CHL1_uc011asi.1_Intron|uc003box.1_Intron	NM_006614	NP_006605			cell adhesion molecule with homology to L1CAM						axon guidance|cell adhesion|signal transduction	integral to membrane|plasma membrane|proteinaceous extracellular matrix				skin(5)|central_nervous_system(4)|large_intestine(2)|ovary(1)	12		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	1130440	1130442	+	IGR	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1130440_1130442delTTT								CHL1 (679345 upstream) : CNTN6 (4178 downstream)																																			---	---	---	---
CNTN4	152330	broad.mit.edu	37	3	2748990	2748990	+	Intron	DEL	A	-	-	rs79883716		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2748990delA	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	2781715	2781715	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2781715delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	3282638	3282638	+	IGR	DEL	G	-	-	rs10713562		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3282638delG								CRBN (61248 upstream) : SUMF1 (540398 downstream)																																			---	---	---	---
SUMF1	285362	broad.mit.edu	37	3	3824479	3824480	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3824479_3824480delAA	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	4325936	4325936	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4325936delA	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)														---	---	---	---
ITPR1	3708	broad.mit.edu	37	3	4792112	4792112	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4792112delT	uc003bqa.2	+						ITPR1_uc010hca.1_Intron|ITPR1_uc011asu.1_Intron|ITPR1_uc003bqc.2_Intron|EGOT_uc003bqd.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	5019158	5019158	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5019158delT	uc003bqe.1	-						uc010hce.1_Intron|BHLHE40_uc003bqf.2_5'Flank|BHLHE40_uc011asw.1_5'Flank					Homo sapiens cDNA FLJ32330 fis, clone PROST2004742.																												OREG0031797	type=REGULATORY REGION|TFbs=RELA|Dataset=RELA (p65) ChIP-PET Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with paired-end diTag sequencing (ChIP-PET)	---	---	---	---
Unknown	0	broad.mit.edu	37	3	5722682	5722682	+	IGR	DEL	T	-	-	rs67765105		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5722682delT								EDEM1 (461033 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	6379406	6379406	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:6379406delT								None (None upstream) : GRM7 (523396 downstream)																																			---	---	---	---
GRM7	2917	broad.mit.edu	37	3	7454673	7454674	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7454673_7454674delAC	uc003bqm.2	+						GRM7_uc011ata.1_Intron|GRM7_uc011atb.1_Intron|GRM7_uc010hcf.2_Intron|GRM7_uc011atc.1_Intron|GRM7_uc010hcg.2_Intron|GRM7_uc003bql.2_Intron|GRM7_uc003bqn.1_Intron	NM_000844	NP_000835			glutamate receptor, metabotropic 7 isoform a						negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	8134962	8134962	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8134962delA								GRM7 (351744 upstream) : LMCD1 (408549 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	8150015	8150015	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8150015delT								GRM7 (366797 upstream) : LMCD1 (393496 downstream)																																			---	---	---	---
C3orf32	51066	broad.mit.edu	37	3	8757754	8757754	+	Intron	DEL	A	-	-	rs75572814	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8757754delA	uc003bqz.2	-							NM_015931	NP_057015			hypothetical protein LOC51066											skin(1)	1																		---	---	---	---
SRGAP3	9901	broad.mit.edu	37	3	9101023	9101024	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9101023_9101024insA	uc003brf.1	-						SRGAP3_uc003brg.1_Intron|SRGAP3_uc003bri.1_Intron|SRGAP3_uc003brk.2_3'UTR|SRGAP3_uc003brj.1_Intron	NM_014850	NP_055665			SLIT-ROBO Rho GTPase activating protein 3						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding		SRGAP3/RAF1(4)	central_nervous_system(4)|skin(3)|urinary_tract(1)|breast(1)	9				OV - Ovarian serous cystadenocarcinoma(96;0.0563)				T	RAF1	pilocytic astrocytoma								---	---	---	---
Unknown	0	broad.mit.edu	37	3	9648583	9648584	+	IGR	DEL	TA	-	-	rs35598236		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9648583_9648584delTA								LHFPL4 (53097 upstream) : MTMR14 (42560 downstream)																																			---	---	---	---
CRELD1	78987	broad.mit.edu	37	3	9980681	9980681	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9980681delA	uc003bug.2	+						CIDEC_uc003bto.2_Intron|CRELD1_uc003buf.2_Intron|CRELD1_uc003buh.2_Intron|CRELD1_uc003bui.2_Intron|CRELD1_uc003buj.2_Intron	NM_001077415	NP_001070883			cysteine-rich with EGF-like domains 1 isoform 3						cardiac septum development|endocardial cushion development	integral to membrane	calcium ion binding			ovary(1)	1																		---	---	---	---
FANCD2	2177	broad.mit.edu	37	3	10143086	10143087	+	3'UTR	INS	-	A	A	rs138111025	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10143086_10143087insA	uc003bux.1	+	44					FANCD2_uc003buy.1_3'UTR|FANCD2_uc010hcw.1_RNA|C3orf24_uc003buz.2_Intron	NM_001018115	NP_001018125			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				---	---	---	---
ATG7	10533	broad.mit.edu	37	3	11541879	11541879	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11541879delA	uc003bwc.2	+						ATG7_uc003bwd.2_Intron|ATG7_uc011aum.1_Intron	NM_006395	NP_006386			APG7 autophagy 7-like isoform a						autophagy|cellular membrane fusion|positive regulation of protein modification process|protein lipidation|protein transport	cytoplasm	APG12 activating enzyme activity|protein homodimerization activity|ubiquitin activating enzyme activity			central_nervous_system(1)	1																		---	---	---	---
ATG7	10533	broad.mit.edu	37	3	11579967	11579967	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11579967delA	uc003bwc.2	+						ATG7_uc003bwd.2_Intron|ATG7_uc011aum.1_Intron|uc003bwe.1_RNA	NM_006395	NP_006386			APG7 autophagy 7-like isoform a						autophagy|cellular membrane fusion|positive regulation of protein modification process|protein lipidation|protein transport	cytoplasm	APG12 activating enzyme activity|protein homodimerization activity|ubiquitin activating enzyme activity			central_nervous_system(1)	1																		---	---	---	---
C3orf31	132001	broad.mit.edu	37	3	11848924	11848927	+	Intron	DEL	CACT	-	-	rs3839098		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11848924_11848927delCACT	uc003bwh.2	-						C3orf31_uc003bwj.2_Intron|C3orf31_uc003bwi.2_Intron|C3orf31_uc011auo.1_Frame_Shift_Del_p.L439fs	NM_138807	NP_620162			MMP37-like protein, mitochondrial precursor						protein import into mitochondrial matrix	extrinsic to mitochondrial inner membrane					0																		---	---	---	---
C3orf31	132001	broad.mit.edu	37	3	11849398	11849398	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11849398delA	uc003bwh.2	-						C3orf31_uc003bwj.2_Intron|C3orf31_uc003bwi.2_Intron|C3orf31_uc011auo.1_Intron	NM_138807	NP_620162			MMP37-like protein, mitochondrial precursor						protein import into mitochondrial matrix	extrinsic to mitochondrial inner membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	11933141	11933141	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11933141delA								C3orf31 (44789 upstream) : SYN2 (112721 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	12317664	12317665	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12317664_12317665delAA								SYN2 (84134 upstream) : PPARG (11684 downstream)																																			---	---	---	---
PPARG	5468	broad.mit.edu	37	3	12388096	12388097	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12388096_12388097delTT	uc003bwr.2	+						PPARG_uc003bws.2_Intron|PPARG_uc003bwu.2_Intron|PPARG_uc003bwv.2_Intron|PPARG_uc003bwq.1_Intron|PPARG_uc010hdz.1_Intron|PPARG_uc003bwt.1_Intron	NM_138712	NP_619726			peroxisome proliferative activated receptor						activation of caspase activity|cell fate commitment|cell maturation|cellular response to insulin stimulus|epithelial cell differentiation|glucose homeostasis|induction of apoptosis|innate immune response|lipid homeostasis|lipoprotein transport|long-chain fatty acid transport|low-density lipoprotein particle receptor biosynthetic process|monocyte differentiation|negative regulation of cholesterol storage|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of macrophage derived foam cell differentiation|negative regulation of receptor biosynthetic process|negative regulation of sequestering of triglyceride|negative regulation of transcription from RNA polymerase II promoter|placenta development|positive regulation of fat cell differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to lipid|response to low-density lipoprotein particle stimulus|white fat cell differentiation	cytosol|nucleoplasm	activating transcription factor binding|arachidonic acid binding|drug binding|enzyme binding|prostaglandin receptor activity|retinoid X receptor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|kidney(1)	2					Atorvastatin(DB01076)|Icosapent(DB00159)|Pioglitazone(DB01132)|Rosiglitazone(DB00412)|Troglitazone(DB00197)			T	PAX8	follicular thyroid		Insulin resistance ; lipodystrophy|familial partial L;diabetes mellitus|insulin-resistantI|with acanthosis nigricans and hypertension						---	---	---	---
MKRN2	23609	broad.mit.edu	37	3	12612632	12612633	+	Intron	INS	-	T	T	rs114189914		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12612632_12612633insT	uc003bxd.2	+						MKRN2_uc003bxe.2_Intron|MKRN2_uc011aus.1_Intron	NM_014160	NP_054879			makorin ring finger protein 2							intracellular	ligase activity|nucleic acid binding|zinc ion binding				0																		---	---	---	---
MKRN2	23609	broad.mit.edu	37	3	12613002	12613002	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12613002delC	uc003bxd.2	+						MKRN2_uc003bxe.2_Intron|MKRN2_uc011aus.1_Intron	NM_014160	NP_054879			makorin ring finger protein 2							intracellular	ligase activity|nucleic acid binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	12723608	12723609	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12723608_12723609delAA								RAF1 (17908 upstream) : TMEM40 (51783 downstream)																																			---	---	---	---
IQSEC1	9922	broad.mit.edu	37	3	13052193	13052193	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13052193delT	uc011auw.1	-							NM_001134382	NP_001127854			IQ motif and Sec7 domain 1 isoform a						regulation of ARF protein signal transduction	cytoplasm|nucleus	ARF guanyl-nucleotide exchange factor activity			ovary(1)	1																		---	---	---	---
NUP210	23225	broad.mit.edu	37	3	13451341	13451342	+	Intron	DEL	TT	-	-	rs67505054		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13451341_13451342delTT	uc003bxv.1	-							NM_024923	NP_079199			nucleoporin 210 precursor						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	endoplasmic reticulum membrane|nuclear membrane|nuclear pore				ovary(3)|large_intestine(3)|skin(3)|pancreas(1)|liver(1)	11	all_neural(104;0.187)																	---	---	---	---
Unknown	0	broad.mit.edu	37	3	13487028	13487028	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13487028delA								NUP210 (25219 upstream) : HDAC11 (34196 downstream)																																			---	---	---	---
LOC285375	285375	broad.mit.edu	37	3	13747501	13747501	+	Intron	DEL	T	-	-	rs13062791	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13747501delT	uc003byd.1	+							NR_027103				Homo sapiens, clone IMAGE:5742174, mRNA.												0																		---	---	---	---
WNT7A	7476	broad.mit.edu	37	3	13902379	13902379	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13902379delC	uc003bye.1	-							NM_004625	NP_004616			wingless-type MMTV integration site family,						activation of JUN kinase activity|anterior/posterior pattern formation|canonical Wnt receptor signaling pathway|cell proliferation in forebrain|cellular response to transforming growth factor beta stimulus|central nervous system vasculogenesis|cerebellar granule cell differentiation|dorsal/ventral pattern formation|embryonic axis specification|embryonic digit morphogenesis|embryonic forelimb morphogenesis|embryonic leg morphogenesis|lens fiber cell development|negative regulation of neurogenesis|palate development|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of epithelial cell proliferation involved in wound healing|positive regulation of JNK cascade|positive regulation of synaptogenesis|positive regulation of transcription from RNA polymerase II promoter|regulation of axon diameter|satellite cell activation|satellite cell maintenance involved in skeletal muscle regeneration|sex differentiation|uterus development|Wnt receptor signaling pathway involved in wound healing, spreading of epidermal cells|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	cytokine activity|frizzled binding|receptor agonist activity|signal transducer activity			ovary(2)|breast(1)	3																		---	---	---	---
TPRXL	348825	broad.mit.edu	37	3	13978445	13978445	+	5'Flank	DEL	A	-	-	rs11328893		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13978445delA	uc011avd.1	+							NR_002223				RecName: Full=Putative protein TPRXL;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	14360522	14360522	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14360522delT								LSM3 (120686 upstream) : SLC6A6 (83584 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	15688174	15688174	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15688174delT								BTD (850 upstream) : ANKRD28 (20570 downstream)																																			---	---	---	---
ANKRD28	23243	broad.mit.edu	37	3	15719917	15719917	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15719917delA	uc003caj.1	-						ANKRD28_uc003cai.1_Intron|ANKRD28_uc011avz.1_Intron|ANKRD28_uc003cak.1_Intron|ANKRD28_uc011awa.1_Intron|ANKRD28_uc011avy.1_5'Flank	NM_015199	NP_056014			ankyrin repeat domain 28							nucleoplasm	protein binding			breast(1)	1																		---	---	---	---
ANKRD28	23243	broad.mit.edu	37	3	15720643	15720645	+	Intron	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15720643_15720645delTTT	uc003caj.1	-						ANKRD28_uc003cai.1_Intron|ANKRD28_uc011avz.1_Intron|ANKRD28_uc003cak.1_Intron|ANKRD28_uc011awa.1_Intron|ANKRD28_uc011avy.1_5'Flank	NM_015199	NP_056014			ankyrin repeat domain 28							nucleoplasm	protein binding			breast(1)	1																		---	---	---	---
GALNTL2	117248	broad.mit.edu	37	3	16053713	16053714	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16053713_16053714delTT	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	16249823	16249823	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16249823delT	uc003car.3	+						GALNTL2_uc003caq.3_Intron	NM_054110	NP_473451			UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane|transport vesicle	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(1)	1																		---	---	---	---
RFTN1	23180	broad.mit.edu	37	3	16406691	16406692	+	Intron	INS	-	A	A	rs143773309	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16406691_16406692insA	uc003cay.2	-						RFTN1_uc010hes.2_Intron	NM_015150	NP_055965			raft-linking protein							plasma membrane				ovary(3)|central_nervous_system(1)	4																		---	---	---	---
RFTN1	23180	broad.mit.edu	37	3	16476153	16476153	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16476153delA	uc003cay.2	-						RFTN1_uc010hes.2_Intron	NM_015150	NP_055965			raft-linking protein							plasma membrane				ovary(3)|central_nervous_system(1)	4																		---	---	---	---
RFTN1	23180	broad.mit.edu	37	3	16528477	16528477	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16528477delC	uc003cay.2	-							NM_015150	NP_055965			raft-linking protein							plasma membrane				ovary(3)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	17145541	17145541	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17145541delA								PLCL2 (13444 upstream) : TBC1D5 (53114 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	17971052	17971052	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17971052delT								TBC1D5 (186812 upstream) : SATB1 (418214 downstream)																																			---	---	---	---
SATB1	6304	broad.mit.edu	37	3	18390354	18390354	+	3'UTR	DEL	A	-	-	rs71703106		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18390354delA	uc003cbh.2	-	11					SATB1_uc003cbi.2_3'UTR|SATB1_uc003cbj.2_3'UTR	NM_002971	NP_002962			special AT-rich sequence binding protein 1						cellular component disassembly involved in apoptosis|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter	nuclear matrix|PML body	double-stranded DNA binding|sequence-specific DNA binding			skin(2)|ovary(1)|lung(1)	4																		---	---	---	---
SATB1	6304	broad.mit.edu	37	3	18422214	18422214	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18422214delT	uc003cbh.2	-						SATB1_uc003cbi.2_Intron|SATB1_uc003cbj.2_Intron	NM_002971	NP_002962			special AT-rich sequence binding protein 1						cellular component disassembly involved in apoptosis|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter	nuclear matrix|PML body	double-stranded DNA binding|sequence-specific DNA binding			skin(2)|ovary(1)|lung(1)	4																		---	---	---	---
KCNH8	131096	broad.mit.edu	37	3	19431956	19431956	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19431956delT	uc003cbk.1	+						KCNH8_uc011awe.1_Intron|KCNH8_uc010hex.1_Intron|KCNH8_uc011awf.1_5'Flank	NM_144633	NP_653234			potassium voltage-gated channel, subfamily H,							integral to membrane	two-component sensor activity			lung(4)|ovary(1)	5																		---	---	---	---
KCNH8	131096	broad.mit.edu	37	3	19551493	19551494	+	Intron	DEL	GA	-	-	rs59753572		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19551493_19551494delGA	uc003cbk.1	+						KCNH8_uc010hex.1_Intron	NM_144633	NP_653234			potassium voltage-gated channel, subfamily H,							integral to membrane	two-component sensor activity			lung(4)|ovary(1)	5																		---	---	---	---
KAT2B	8850	broad.mit.edu	37	3	20152984	20152984	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20152984delT	uc003cbq.2	+							NM_003884	NP_003875			K(lysine) acetyltransferase 2B						cell cycle arrest|cellular response to insulin stimulus|chromatin remodeling|histone H3 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|negative regulation of cell proliferation|transcription initiation from RNA polymerase I promoter	Ada2/Gcn5/Ada3 transcription activator complex|chromatin remodeling complex|PCAF complex	cyclin-dependent protein kinase inhibitor activity|histone acetyltransferase activity|histone deacetylase binding|protein kinase binding|transcription coactivator activity|transcription factor binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	20474053	20474054	+	IGR	INS	-	C	C	rs146694664	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20474053_20474054insC								SGOL1 (246370 upstream) : VENTXP7 (973164 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	20963950	20963951	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20963950_20963951delAA								SGOL1 (736267 upstream) : VENTXP7 (483267 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	21068492	21068495	+	IGR	DEL	TGTG	-	-	rs35807341		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:21068492_21068495delTGTG								SGOL1 (840809 upstream) : VENTXP7 (378723 downstream)																																			---	---	---	---
ZNF385D	79750	broad.mit.edu	37	3	21531823	21531824	+	Intron	INS	-	TT	TT			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:21531823_21531824insTT	uc003cce.2	-						ZNF385D_uc010hfb.1_Intron	NM_024697	NP_078973			zinc finger protein 385D							nucleus	nucleic acid binding|zinc ion binding			large_intestine(2)|skin(2)|ovary(1)	5																		---	---	---	---
ZNF385D	79750	broad.mit.edu	37	3	21756801	21756801	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:21756801delT	uc003cce.2	-						ZNF385D_uc010hfb.1_Intron	NM_024697	NP_078973			zinc finger protein 385D							nucleus	nucleic acid binding|zinc ion binding			large_intestine(2)|skin(2)|ovary(1)	5																		---	---	---	---
ZNF385D	79750	broad.mit.edu	37	3	21774300	21774300	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:21774300delT	uc003cce.2	-						ZNF385D_uc010hfb.1_Intron	NM_024697	NP_078973			zinc finger protein 385D							nucleus	nucleic acid binding|zinc ion binding			large_intestine(2)|skin(2)|ovary(1)	5																		---	---	---	---
ZNF385D	79750	broad.mit.edu	37	3	22045365	22045365	+	Intron	DEL	A	-	-	rs34327227		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:22045365delA	uc010hfb.1	-											Homo sapiens cDNA: FLJ22419 fis, clone HRC08593.							nucleus	nucleic acid binding|zinc ion binding			large_intestine(2)|skin(2)|ovary(1)	5																		---	---	---	---
ZNF385D	79750	broad.mit.edu	37	3	22186502	22186503	+	Intron	INS	-	TGTG	TGTG	rs151115648	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:22186502_22186503insTGTG	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	23058048	23058051	+	IGR	DEL	ATGG	-	-	rs80172204		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23058048_23058051delATGG								ZNF385D (643925 upstream) : UBE2E2 (186602 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	23205687	23205687	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23205687delA								ZNF385D (791564 upstream) : UBE2E2 (38966 downstream)																																			---	---	---	---
UBE2E1	7324	broad.mit.edu	37	3	23930592	23930593	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23930592_23930593insT	uc003cch.2	+						UBE2E1_uc003cci.2_Intron|UBE2E1_uc011awh.1_Intron	NM_003341	NP_003332			ubiquitin-conjugating enzyme E2E 1 isoform 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|histone H2B ubiquitination|histone monoubiquitination|ISG15-protein conjugation|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K48-linked ubiquitination	cytosol|nucleoplasm|ubiquitin ligase complex	ATP binding|ISG15 ligase activity|protein binding|ubiquitin-protein ligase activity				0																		---	---	---	---
THRB	7068	broad.mit.edu	37	3	24310889	24310898	+	Intron	DEL	CGCGCGCACA	-	-	rs72187943		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24310889_24310898delCGCGCGCACA	uc003ccx.3	-						THRB_uc010hfe.2_Intron|THRB_uc003ccy.3_Intron|THRB_uc003ccz.3_Intron|THRB_uc003cdc.2_Intron|THRB_uc003cdd.2_Intron|THRB_uc003cde.1_Intron	NM_001128176	NP_001121648			thyroid hormone receptor, beta						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	enzyme binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|thyroid hormone receptor activity|transcription corepressor activity|zinc ion binding			skin(2)|pancreas(1)	3					Levothyroxine(DB00451)|Liothyronine(DB00279)													---	---	---	---
THRB	7068	broad.mit.edu	37	3	24361157	24361157	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24361157delA	uc003ccx.3	-						THRB_uc010hfe.2_Intron|THRB_uc003ccy.3_Intron|THRB_uc003ccz.3_Intron|THRB_uc003cdc.2_Intron|THRB_uc003cdd.2_Intron|THRB_uc003cde.1_Intron	NM_001128176	NP_001121648			thyroid hormone receptor, beta						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	enzyme binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|thyroid hormone receptor activity|transcription corepressor activity|zinc ion binding			skin(2)|pancreas(1)	3					Levothyroxine(DB00451)|Liothyronine(DB00279)													---	---	---	---
LRRC3B	116135	broad.mit.edu	37	3	26694842	26694842	+	Intron	DEL	T	-	-	rs111673556		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:26694842delT	uc003cdp.2	+						LRRC3B_uc003cdq.2_Intron	NM_052953	NP_443185			leucine rich repeat containing 3B precursor							integral to membrane				pancreas(2)|ovary(1)|skin(1)	4																		---	---	---	---
CMC1	152100	broad.mit.edu	37	3	28284549	28284549	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:28284549delT	uc003cea.2	+							NM_182523	NP_872329			COX assembly mitochondrial protein homolog							mitochondrion	metal ion binding				0																		---	---	---	---
RBMS3	27303	broad.mit.edu	37	3	29586190	29586191	+	Intron	INS	-	TG	TG	rs138879910	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:29586190_29586191insTG	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	29940227	29940228	+	Intron	INS	-	GT	GT	rs145413086	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:29940227_29940228insGT	uc003cel.2	+						RBMS3_uc003cek.2_Intron|RBMS3_uc010hfq.2_Intron|RBMS3_uc003cem.2_Intron|RBMS3_uc010hfr.2_Intron	NM_001003793	NP_001003793			RNA binding motif, single stranded interacting							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)	1		Ovarian(412;0.0956)																---	---	---	---
Unknown	0	broad.mit.edu	37	3	30589347	30589358	+	IGR	DEL	TGACAGTGCCAT	-	-	rs148530180		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30589347_30589358delTGACAGTGCCAT								RBMS3 (542728 upstream) : TGFBR2 (58636 downstream)																																			---	---	---	---
OSBPL10	114884	broad.mit.edu	37	3	31792636	31792636	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31792636delA	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	31924736	31924738	+	Intron	DEL	TTT	-	-	rs34333418		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31924736_31924738delTTT	uc003cev.2	-						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	31980949	31980949	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31980949delA	uc003cev.2	-						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)														---	---	---	---
CMTM8	152189	broad.mit.edu	37	3	32301786	32301786	+	Intron	DEL	A	-	-	rs6796318	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32301786delA	uc003cex.2	+						CMTM8_uc010hfu.2_Intron	NM_178868	NP_849199			CKLF-like MARVEL transmembrane domain containing						chemotaxis	extracellular space|integral to membrane	cytokine activity				0																		---	---	---	---
CMTM7	112616	broad.mit.edu	37	3	32432980	32432980	+	5'Flank	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32432980delG	uc003cey.1	+						CMTM7_uc003cez.1_5'Flank	NM_138410	NP_612419			CKLF-like MARVEL transmembrane domain containing						chemotaxis	extracellular space|integral to membrane	cytokine activity				0																		---	---	---	---
DYNC1LI1	51143	broad.mit.edu	37	3	32603121	32603122	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32603121_32603122delAA	uc003cfb.3	-						DYNC1LI1_uc011axh.1_Intron	NM_016141	NP_057225			dynein, cytoplasmic 1, light intermediate chain						cell division|interspecies interaction between organisms|mitosis|positive regulation of mitotic cell cycle spindle assembly checkpoint|transport	centrosome|condensed chromosome kinetochore|cytoplasmic dynein complex|microtubule|plasma membrane|spindle pole	ATP binding|motor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	32827634	32827635	+	IGR	DEL	AT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32827634_32827635delAT								CNOT10 (12280 upstream) : TRIM71 (31875 downstream)																																			---	---	---	---
TRIM71	131405	broad.mit.edu	37	3	32890854	32890854	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32890854delT	uc003cff.2	+							NM_001039111	NP_001034200			tripartite motif-containing 71						multicellular organismal development	cytoplasm	zinc ion binding			ovary(2)|large_intestine(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	32975244	32975244	+	IGR	DEL	A	-	-	rs78314440		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32975244delA								TRIM71 (41474 upstream) : CCR4 (17822 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	33018701	33018703	+	IGR	DEL	TTT	-	-	rs63564061		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33018701_33018703delTTT								CCR4 (22298 upstream) : GLB1 (19397 downstream)																																			---	---	---	---
GLB1	2720	broad.mit.edu	37	3	33118553	33118553	+	Intron	DEL	A	-	-	rs112485906		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33118553delA	uc003cfi.1	-						GLB1_uc003cfh.1_Intron|GLB1_uc003cfj.1_Intron|GLB1_uc011axk.1_Intron	NM_000404	NP_000395			galactosidase, beta 1 isoform a preproprotein						carbohydrate metabolic process	lysosome|perinuclear region of cytoplasm	beta-galactosidase activity|cation binding|protein binding			large_intestine(1)	1		Melanoma(143;0.104)																---	---	---	---
UBP1	7342	broad.mit.edu	37	3	33457246	33457246	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33457246delA	uc003cfq.3	-						UBP1_uc003cfr.3_Intron|UBP1_uc010hga.2_Intron	NM_014517	NP_055332			upstream binding protein 1 (LBP-1a) isoform a						negative regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|viral genome replication	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			kidney(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	34225961	34225961	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34225961delT								PDCD6IP (314767 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	34294068	34294070	+	IGR	DEL	TTT	-	-	rs75037947		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34294068_34294070delTTT								PDCD6IP (382874 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	34626912	34626912	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34626912delT								PDCD6IP (715718 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	34842681	34842682	+	IGR	INS	-	CTGC	CTGC	rs140064109	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34842681_34842682insCTGC								PDCD6IP (931487 upstream) : ARPP21 (838399 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	35256942	35256942	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35256942delT								None (None upstream) : ARPP21 (424139 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	35439981	35439982	+	IGR	INS	-	AC	AC			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35439981_35439982insAC								None (None upstream) : ARPP21 (241099 downstream)																																			---	---	---	---
ARPP21	10777	broad.mit.edu	37	3	35717290	35717291	+	Intron	INS	-	GAT	GAT	rs138655463	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35717290_35717291insGAT	uc003cgb.2	+						ARPP21_uc003cga.2_Intron|ARPP21_uc003cfz.2_Intron	NM_016300	NP_057384			cyclic AMP-regulated phosphoprotein, 21 kD							cytoplasm	nucleic acid binding			ovary(2)|skin(1)	3																		---	---	---	---
STAC	6769	broad.mit.edu	37	3	36578345	36578345	+	Intron	DEL	A	-	-	rs4678885		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36578345delA	uc003cgh.1	+						STAC_uc011aya.1_Intron	NM_003149	NP_003140			SH3 and cysteine rich domain						intracellular signal transduction	cytoplasm|soluble fraction	metal ion binding			skin(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	37238346	37238346	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37238346delA								LRRFIP2 (20495 upstream) : GOLGA4 (46392 downstream)																																			---	---	---	---
ITGA9	3680	broad.mit.edu	37	3	37857411	37857411	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37857411delA	uc003chd.2	+						uc003che.2_Intron	NM_002207	NP_002198			integrin, alpha 9 precursor						axon guidance|cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			breast(3)|pancreas(1)|lung(1)|skin(1)	6				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)														---	---	---	---
CTDSPL	10217	broad.mit.edu	37	3	37951217	37951218	+	Intron	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37951217_37951218delTG	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	37981583	37981583	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37981583delA	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	38006176	38006176	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38006176delA	uc003chg.2	+						CTDSPL_uc003chh.2_Intron|CTDSPL_uc003chi.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)														---	---	---	---
SCN5A	6331	broad.mit.edu	37	3	38627963	38627963	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38627963delG	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)													---	---	---	---
SCN10A	6336	broad.mit.edu	37	3	38778314	38778314	+	Intron	DEL	G	-	-	rs34074715		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38778314delG	uc003ciq.2	-							NM_006514	NP_006505			sodium channel, voltage-gated, type X, alpha						sensory perception	voltage-gated sodium channel complex				ovary(5)|skin(3)|large_intestine(1)|kidney(1)	10				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dibucaine(DB00527)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)													---	---	---	---
SCN10A	6336	broad.mit.edu	37	3	38808534	38808535	+	Intron	INS	-	T	T	rs146346987	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38808534_38808535insT	uc003ciq.2	-							NM_006514	NP_006505			sodium channel, voltage-gated, type X, alpha						sensory perception	voltage-gated sodium channel complex				ovary(5)|skin(3)|large_intestine(1)|kidney(1)	10				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dibucaine(DB00527)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	38862640	38862640	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38862640delC								SCN10A (27139 upstream) : SCN11A (24620 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	39237877	39237877	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39237877delT								XIRP1 (3800 upstream) : CX3CR1 (67109 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	39270188	39270188	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39270188delT								XIRP1 (36111 upstream) : CX3CR1 (34798 downstream)																																			---	---	---	---
MYRIP	25924	broad.mit.edu	37	3	40023419	40023420	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40023419_40023420delAC	uc003cka.2	+						MYRIP_uc010hhu.2_Intron|MYRIP_uc010hhv.2_Intron|MYRIP_uc010hhw.2_Intron|MYRIP_uc010hhx.1_Intron	NM_015460	NP_056275			myosin VIIA and Rab interacting protein						intracellular protein transport		actin binding|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5				KIRC - Kidney renal clear cell carcinoma(284;0.174)|Kidney(284;0.206)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	40348193	40348194	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40348193_40348194insA	uc003ckb.2	-						EIF1B_uc003ckc.2_5'Flank					Homo sapiens cDNA FLJ33065 fis, clone TRACH2000081.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	40385486	40385486	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40385486delT								EIF1B (31573 upstream) : ENTPD3 (43187 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	40413754	40413754	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40413754delG								EIF1B (59841 upstream) : ENTPD3 (14919 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	41066464	41066465	+	IGR	DEL	AA	-	-	rs59557163		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41066464_41066465delAA								ZNF621 (485421 upstream) : CTNNB1 (169936 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	41207125	41207126	+	IGR	DEL	TA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41207125_41207126delTA								ZNF621 (626082 upstream) : CTNNB1 (29275 downstream)																																			---	---	---	---
ULK4	54986	broad.mit.edu	37	3	41789171	41789171	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41789171delG	uc003ckv.3	-							NM_017886	NP_060356			unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	42023526	42023526	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42023526delT								ULK4 (19866 upstream) : TRAK1 (109220 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	43178223	43178223	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43178223delT								C3orf39 (30658 upstream) : SNRK (149781 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	43400292	43400292	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43400292delA								SNRK (7660 upstream) : ANO10 (7527 downstream)																																			---	---	---	---
ANO10	55129	broad.mit.edu	37	3	43545772	43545773	+	Intron	INS	-	TAGG	TAGG			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43545772_43545773insTAGG	uc003cmv.2	-						ANO10_uc011azs.1_Intron|ANO10_uc003cmw.2_Intron|ANO10_uc010hil.2_Intron|ANO10_uc011azt.1_Intron	NM_018075	NP_060545			transmembrane protein 16K						cell death	chloride channel complex	chloride channel activity			ovary(2)	2																		---	---	---	---
C3orf77	375337	broad.mit.edu	37	3	44281350	44281355	+	5'Flank	DEL	GTGTGT	-	-	rs59344463		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44281350_44281355delGTGTGT	uc003cna.3	+							NM_001145030	NP_001138502			hypothetical protein LOC375337											pancreas(1)	1																		---	---	---	---
KIF15	56992	broad.mit.edu	37	3	44815872	44815872	+	Intron	DEL	T	-	-	rs112868991		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44815872delT	uc003cnx.3	+						KIF15_uc010hiq.2_Intron	NM_020242	NP_064627			kinesin family member 15						blood coagulation|cell proliferation|microtubule-based movement|mitosis	centrosome|cytosol|microtubule|plus-end kinesin complex|spindle	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	45321547	45321547	+	IGR	DEL	C	-	-	rs34904645		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45321547delC								TMEM158 (53733 upstream) : LARS2 (108528 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	45397136	45397136	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45397136delA								TMEM158 (129322 upstream) : LARS2 (32939 downstream)																																			---	---	---	---
LTF	4057	broad.mit.edu	37	3	46481401	46481401	+	Intron	DEL	A	-	-	rs112263753		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46481401delA	uc003cpq.2	-						LTF_uc003fzr.2_Intron|LTF_uc010hjh.2_Intron|LTF_uc003cpr.2_Intron	NM_002343	NP_002334			lactotransferrin precursor						cellular iron ion homeostasis|defense response to bacterium|humoral immune response|iron ion transport	extracellular region|stored secretory granule	ferric iron binding|heparin binding|protein binding|serine-type endopeptidase activity			central_nervous_system(2)|ovary(1)|lung(1)	4				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)	Pefloxacin(DB00487)													---	---	---	---
SETD2	29072	broad.mit.edu	37	3	47176125	47176125	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47176125delT	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								---	---	---	---
SCAP	22937	broad.mit.edu	37	3	47466549	47466549	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47466549delA	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)														---	---	---	---
MAP4	4134	broad.mit.edu	37	3	48092583	48092584	+	Intron	DEL	CA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48092583_48092584delCA	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)														---	---	---	---
DAG1	1605	broad.mit.edu	37	3	49518079	49518079	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49518079delT	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)														---	---	---	---
CDHR4	389118	broad.mit.edu	37	3	49833796	49833796	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49833796delT	uc010hkz.2	-							NM_001007540	NP_001007541			cadherin-like 29 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0																		---	---	---	---
CACNA2D2	9254	broad.mit.edu	37	3	50411305	50411306	+	Intron	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50411305_50411306delAG	uc003daq.2	-						CACNA2D2_uc003dap.2_Intron	NM_006030	NP_006021			calcium channel, voltage-dependent, alpha						energy reserve metabolic process|regulation of insulin secretion	integral to membrane|plasma membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000365)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)	Gabapentin(DB00996)													---	---	---	---
CACNA2D2	9254	broad.mit.edu	37	3	50493325	50493325	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50493325delC	uc003daq.2	-						CACNA2D2_uc003dap.2_Intron	NM_006030	NP_006021			calcium channel, voltage-dependent, alpha						energy reserve metabolic process|regulation of insulin secretion	integral to membrane|plasma membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000365)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)	Gabapentin(DB00996)													---	---	---	---
RAD54L2	23132	broad.mit.edu	37	3	51576466	51576467	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51576466_51576467delTT	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)														---	---	---	---
IQCF1	132141	broad.mit.edu	37	3	51867976	51867977	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51867976_51867977delTT	uc003dbq.3	-											Homo sapiens cDNA FLJ27508 fis, clone TST08061.											ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000541)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)														---	---	---	---
PHF7	51533	broad.mit.edu	37	3	52455587	52455587	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52455587delG	uc003ddy.2	+						PHF7_uc003ddz.2_Intron	NM_016483	NP_057567			PHD finger protein 7 isoform 1							nucleus	zinc ion binding			breast(1)	1				BRCA - Breast invasive adenocarcinoma(193;1.71e-05)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)|OV - Ovarian serous cystadenocarcinoma(275;0.0275)														---	---	---	---
STAB1	23166	broad.mit.edu	37	3	52551796	52551796	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52551796delG	uc003dej.2	+						STAB1_uc003dek.1_5'Flank	NM_015136	NP_055951			stabilin 1 precursor						cell adhesion|cell-cell signaling|defense response to bacterium|inflammatory response|negative regulation of angiogenesis|receptor-mediated endocytosis	integral to plasma membrane	bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			large_intestine(3)|upper_aerodigestive_tract(2)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	9				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)														---	---	---	---
TMEM110	375346	broad.mit.edu	37	3	52884757	52884758	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52884757_52884758insT	uc003dge.2	-						TMEM110_uc003dgc.3_Intron	NM_198563	NP_940965			transmembrane protein 110							integral to membrane				large_intestine(1)	1				BRCA - Breast invasive adenocarcinoma(193;7.72e-05)|Kidney(197;0.000777)|KIRC - Kidney renal clear cell carcinoma(197;0.000915)|OV - Ovarian serous cystadenocarcinoma(275;0.0541)														---	---	---	---
SFMBT1	51460	broad.mit.edu	37	3	52950385	52950396	+	Intron	DEL	TTTTTTTTTTTA	-	-	rs71087030		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52950385_52950396delTTTTTTTTTTTA	uc003dgf.2	-						SFMBT1_uc010hmr.2_Intron|SFMBT1_uc003dgg.2_Intron|SFMBT1_uc003dgh.2_Intron	NM_001005159	NP_001005159			Scm-like with four mbt domains 1						regulation of transcription, DNA-dependent	nucleus				ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;9.91e-05)|Kidney(197;0.000644)|KIRC - Kidney renal clear cell carcinoma(197;0.000792)|OV - Ovarian serous cystadenocarcinoma(275;0.113)														---	---	---	---
RFT1	91869	broad.mit.edu	37	3	53136544	53136545	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53136544_53136545insA	uc003dgj.2	-						RFT1_uc003dgk.2_Intron	NM_052859	NP_443091			RFT1 homolog						carbohydrate transport|dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane	lipid transporter activity			skin(1)	1				BRCA - Breast invasive adenocarcinoma(193;6.98e-05)|Kidney(197;0.0017)|KIRC - Kidney renal clear cell carcinoma(197;0.00192)|OV - Ovarian serous cystadenocarcinoma(275;0.104)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	53407238	53407238	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53407238delT								DCP1A (25601 upstream) : CACNA1D (121793 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	53440755	53440755	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53440755delT								DCP1A (59118 upstream) : CACNA1D (88276 downstream)																																			---	---	---	---
CACNA1D	776	broad.mit.edu	37	3	53531143	53531143	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53531143delA	uc003dgv.3	+						CACNA1D_uc003dgu.3_Intron|CACNA1D_uc003dgy.3_Intron	NM_001128840	NP_001122312			calcium channel, voltage-dependent, L type,						axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(6)|upper_aerodigestive_tract(2)|liver(1)|central_nervous_system(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Verapamil(DB00661)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	54096605	54096606	+	IGR	INS	-	G	G	rs139943984	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54096605_54096606insG								SELK (170616 upstream) : CACNA2D3 (60087 downstream)																																			---	---	---	---
CACNA2D3	55799	broad.mit.edu	37	3	54287812	54287813	+	Intron	INS	-	T	T	rs74643419		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54287812_54287813insT	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	54361822	54361822	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54361822delT	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	54978840	54978847	+	Intron	DEL	GGGTGTGT	-	-	rs111985338		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54978840_54978847delGGGTGTGT	uc003dhf.2	+						CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.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	55041889	55041889	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:55041889delT	uc003dhf.2	+						CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron	NM_018398	NP_060868			calcium channel, voltage-dependent, alpha							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	55383836	55383837	+	IGR	INS	-	A	A	rs11441257		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:55383836_55383837insA								CACNA2D3 (275254 upstream) : WNT5A (115907 downstream)																																			---	---	---	---
ERC2	26059	broad.mit.edu	37	3	55587808	55587808	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:55587808delA	uc003dhr.1	-						ERC2_uc003dho.1_Intron|ERC2_uc003dhp.1_Intron|ERC2_uc003dhq.1_Intron	NM_015576	NP_056391			cytomatrix protein p110							cell junction|cytoplasm|cytoskeleton|growth cone|presynaptic membrane|synaptosome	protein binding			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)														---	---	---	---
C3orf63	23272	broad.mit.edu	37	3	56662794	56662794	+	Intron	DEL	T	-	-	rs35779948		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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)														---	---	---	---
APPL1	26060	broad.mit.edu	37	3	57293836	57293836	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57293836delA	uc003dio.2	+						APPL1_uc010hnb.2_Intron|APPL1_uc011bey.1_Intron	NM_012096	NP_036228			adaptor protein, phosphotyrosine interaction, PH						apoptosis|cell cycle|cell proliferation|insulin receptor signaling pathway|regulation of apoptosis|regulation of establishment of protein localization in plasma membrane|regulation of glucose import	cytosol|early endosome membrane|microsome|nucleus|vesicle membrane	protein kinase B binding			breast(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0124)|Kidney(284;0.0144)														---	---	---	---
DNAH12	201625	broad.mit.edu	37	3	57330291	57330291	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57330291delT	uc003dit.2	-						DNAH12_uc010hnc.2_Intron	NM_178504	NP_848599			dynein heavy chain domain 2 isoform 1						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			pancreas(1)|skin(1)	2																		---	---	---	---
DNAH12	201625	broad.mit.edu	37	3	57477727	57477727	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57477727delA	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																		---	---	---	---
SLMAP	7871	broad.mit.edu	37	3	57850103	57850103	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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)														---	---	---	---
FAM3D	131177	broad.mit.edu	37	3	58620098	58620099	+	Intron	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58620098_58620099delAG	uc003dkq.2	-							NM_138805	NP_620160			family with sequence similarity 3, member D						negative regulation of insulin secretion	extracellular region	cytokine activity				0				BRCA - Breast invasive adenocarcinoma(55;0.000225)|Kidney(10;0.000667)|KIRC - Kidney renal clear cell carcinoma(10;0.000802)|OV - Ovarian serous cystadenocarcinoma(275;0.169)														---	---	---	---
C3orf67	200844	broad.mit.edu	37	3	58892821	58892822	+	Intron	DEL	GT	-	-	rs35001935		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58892821_58892822delGT	uc003dkt.1	-						uc003dku.1_Intron|C3orf67_uc003dkv.1_Intron|C3orf67_uc003dkw.2_Intron|C3orf67_uc011bfg.1_Intron	NM_198463	NP_940865			hypothetical protein LOC200844												0		all_cancers(2;0.000156)|all_epithelial(2;0.000493)|Breast(2;0.00446)|all_lung(2;0.074)|Lung NSC(2;0.248)		BRCA - Breast invasive adenocarcinoma(55;5.93e-06)|Kidney(10;0.00155)|KIRC - Kidney renal clear cell carcinoma(10;0.00172)|OV - Ovarian serous cystadenocarcinoma(275;0.23)														---	---	---	---
FHIT	2272	broad.mit.edu	37	3	60168343	60168343	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:60168343delA	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	60632501	60632501	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:60632501delA	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	60825255	60825255	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:60825255delA	uc003dkx.3	-						FHIT_uc003dky.2_Intron|FHIT_uc010hnn.1_Intron	NM_002012	NP_002003			fragile histidine triad gene						nucleotide metabolic process		bis(5'-adenosyl)-triphosphatase activity|protein binding				0		all_cancers(2;2.37e-314)|all_epithelial(2;5.17e-286)|Colorectal(2;1.24e-68)|all_lung(2;1.31e-45)|Lung NSC(2;1.79e-44)|all_hematologic(2;1.59e-23)|Renal(2;1.03e-13)|Breast(2;1.06e-10)|Esophageal squamous(2;6.31e-09)|Melanoma(2;1.83e-07)|Acute lymphoblastic leukemia(2;5.46e-05)|all_neural(2;0.00118)|Medulloblastoma(2;0.00263)|Hepatocellular(2;0.0245)|Ovarian(2;0.0408)		UCEC - Uterine corpus endometrioid carcinoma (45;0.0887)|Epithelial(1;9.28e-70)|all cancers(1;3.07e-60)|Colorectal(1;2.33e-53)|STAD - Stomach adenocarcinoma(1;7.22e-48)|COAD - Colon adenocarcinoma(3;1.05e-44)|READ - Rectum adenocarcinoma(3;2.41e-08)|KIRC - Kidney renal clear cell carcinoma(10;0.000109)|Kidney(10;0.000125)|Lung(1;0.000161)|LUSC - Lung squamous cell carcinoma(1;0.000742)|OV - Ovarian serous cystadenocarcinoma(275;0.00372)|BRCA - Breast invasive adenocarcinoma(55;0.00448)				T	HMGA2	pleomorphic salivary gland adenoma				Renal_Cell_Cancer_associated_with_constitutional_translocation_of_chromosome_3				---	---	---	---
Unknown	0	broad.mit.edu	37	3	61415824	61415825	+	IGR	INS	-	AC	AC	rs60056333		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:61415824_61415825insAC								FHIT (178691 upstream) : PTPRG (131418 downstream)																																			---	---	---	---
PTPRG	5793	broad.mit.edu	37	3	62278688	62278688	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62278688delT	uc003dlb.2	+						PTPRG_uc003dlc.2_Intron|PTPRG_uc011bfi.1_Intron|uc010hno.2_Intron|uc003dld.3_Intron|uc010hnp.2_Intron|uc003dle.3_Intron	NM_002841	NP_002832			protein tyrosine phosphatase, receptor type, G						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	identical protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(5)|lung(2)	7				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	63178735	63178736	+	IGR	INS	-	G	G	rs145498278	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63178735_63178736insG								LOC285401 (68000 upstream) : SYNPR (85178 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	63620388	63620388	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63620388delA								SYNPR (17792 upstream) : SNTN (17956 downstream)																																			---	---	---	---
PRICKLE2	166336	broad.mit.edu	37	3	64184686	64184686	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64184686delT	uc003dmf.2	-							NM_198859	NP_942559			prickle-like 2							cytoplasm|nuclear membrane	zinc ion binding			ovary(4)|skin(1)	5		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)														---	---	---	---
ADAMTS9	56999	broad.mit.edu	37	3	64547484	64547484	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64547484delG	uc003dmg.2	-						ADAMTS9_uc011bfo.1_Intron|ADAMTS9_uc003dmh.1_Intron|ADAMTS9_uc011bfp.1_Intron|uc003dmi.1_Intron	NM_182920	NP_891550			ADAM metallopeptidase with thrombospondin type 1						glycoprotein catabolic process|multicellular organismal development|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|urinary_tract(1)|skin(1)	4		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	65029257	65029257	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65029257delA								ADAMTS9 (355892 upstream) : MAGI1 (310650 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	65208719	65208720	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65208719_65208720delAA								ADAMTS9 (535354 upstream) : MAGI1 (131187 downstream)																																			---	---	---	---
MAGI1	9223	broad.mit.edu	37	3	65543884	65543884	+	Intron	DEL	C	-	-	rs140787910		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65543884delC	uc003dmn.2	-						MAGI1_uc003dmm.2_Intron|MAGI1_uc003dmo.2_Intron|MAGI1_uc003dmp.2_Intron|MAGI1_uc010hny.2_Intron|MAGI1_uc003dmr.2_Intron	NM_001033057	NP_001028229			membrane associated guanylate kinase, WW and PDZ						cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly	tight junction	ATP binding|protein C-terminus binding			lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1)	6		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)														---	---	---	---
MAGI1	9223	broad.mit.edu	37	3	65941339	65941339	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65941339delA	uc003dmn.2	-						MAGI1_uc003dmm.2_Intron|MAGI1_uc003dmo.2_Intron|MAGI1_uc003dmp.2_Intron|MAGI1_uc003dmr.2_Intron	NM_001033057	NP_001028229			membrane associated guanylate kinase, WW and PDZ						cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly	tight junction	ATP binding|protein C-terminus binding			lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1)	6		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)														---	---	---	---
LRIG1	26018	broad.mit.edu	37	3	66543496	66543496	+	Intron	DEL	G	-	-	rs146249312	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66543496delG	uc003dmx.2	-						LRIG1_uc010hoa.2_Intron	NM_015541	NP_056356			leucine-rich repeats and immunoglobulin-like							integral to membrane				skin(3)|ovary(2)	5		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	66767751	66767751	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66767751delA								LRIG1 (216906 upstream) : KBTBD8 (280976 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	66921991	66921992	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66921991_66921992insA								LRIG1 (371146 upstream) : KBTBD8 (126735 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	66991271	66991271	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66991271delT								LRIG1 (440426 upstream) : KBTBD8 (57456 downstream)																																			---	---	---	---
SUCLG2	8801	broad.mit.edu	37	3	67526144	67526145	+	Intron	DEL	TT	-	-	rs59820958	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67526144_67526145delTT	uc003dna.3	-						SUCLG2_uc010hob.2_Intron	NM_003848	NP_003839			succinate-CoA ligase, GDP-forming beta subunit						succinyl-CoA metabolic process|tricarboxylic acid cycle	mitochondrial matrix	ATP binding|GTP binding|succinate-CoA ligase (GDP-forming) activity			central_nervous_system(1)|skin(1)	2		Renal(2;0.00294)|Lung NSC(201;0.012)|Hepatocellular(537;0.121)		BRCA - Breast invasive adenocarcinoma(55;3.53e-05)|Epithelial(33;0.000153)	Succinic acid(DB00139)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	67991754	67991754	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67991754delT	uc003dnc.2	+											Homo sapiens mRNA; cDNA DKFZp686F1220 (from clone DKFZp686F1220).																														---	---	---	---
UBA3	9039	broad.mit.edu	37	3	69108594	69108595	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69108594_69108595insA	uc003dno.2	-						UBA3_uc003dnq.2_Intron|UBA3_uc011bfy.1_Intron|UBA3_uc011bfz.1_Intron	NM_003968	NP_003959			ubiquitin-activating enzyme 3 isoform 1						protein neddylation|proteolysis	nucleus	acid-amino acid ligase activity|ATP binding|protein heterodimerization activity			ovary(1)	1		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.98e-05)|Epithelial(33;0.000363)|LUSC - Lung squamous cell carcinoma(21;0.012)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.206)|Kidney(39;0.241)														---	---	---	---
FOXP1	27086	broad.mit.edu	37	3	71624593	71624594	+	Intron	INS	-	AC	AC			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71624593_71624594insAC	uc003dop.2	-						FOXP1_uc003doo.2_Intron|FOXP1_uc003dos.2_Intron|uc003dou.2_5'Flank	NM_032682	NP_116071			forkhead box P1 isoform 1						cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)				T	PAX5	ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	3	72925811	72925811	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72925811delT								SHQ1 (28213 upstream) : GXYLT2 (11574 downstream)																																			---	---	---	---
GXYLT2	727936	broad.mit.edu	37	3	73008791	73008791	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73008791delT	uc003dpg.2	+							NM_001080393	NP_001073862			glycosyltransferase 8 domain containing 4						O-glycan processing	integral to membrane	UDP-xylosyltransferase activity				0																		---	---	---	---
GXYLT2	727936	broad.mit.edu	37	3	73016476	73016476	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73016476delT	uc003dpg.2	+							NM_001080393	NP_001073862			glycosyltransferase 8 domain containing 4						O-glycan processing	integral to membrane	UDP-xylosyltransferase activity				0																		---	---	---	---
PDZRN3	23024	broad.mit.edu	37	3	73497742	73497742	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73497742delT	uc003dpl.1	-						PDZRN3_uc011bgh.1_Intron|PDZRN3_uc010hoe.1_Intron|PDZRN3_uc011bgg.1_Intron	NM_015009	NP_055824			PDZ domain containing ring finger 3								ubiquitin-protein ligase activity|zinc ion binding			pancreas(2)|ovary(2)|skin(2)|large_intestine(1)	7		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)														---	---	---	---
CNTN3	5067	broad.mit.edu	37	3	74327406	74327406	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74327406delA	uc003dpm.1	-							NM_020872	NP_065923			contactin 3 precursor						cell adhesion	anchored to membrane|plasma membrane	protein binding			breast(3)|ovary(1)|skin(1)	5		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	75449583	75449584	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75449583_75449584delTG								CNTN3 (879240 upstream) : FAM86D (21121 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	76512534	76512535	+	IGR	INS	-	AAAGT	AAAGT	rs138028487	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76512534_76512535insAAAGT								ZNF717 (677864 upstream) : ROBO2 (576759 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	80501930	80501931	+	IGR	INS	-	TG	TG	rs71633612		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:80501930_80501931insTG								ROBO1 (684871 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	82114264	82114265	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:82114264_82114265delAA	uc003dqh.1	+											Homo sapiens cDNA clone IMAGE:5271111.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	82127727	82127727	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:82127727delA	uc003dqh.1	+											Homo sapiens cDNA clone IMAGE:5271111.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	82177103	82177103	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:82177103delT	uc003dqh.1	+											Homo sapiens cDNA clone IMAGE:5271111.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	82182440	82182440	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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	82216435	82216435	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:82216435delT	uc003dqh.1	+											Homo sapiens cDNA clone IMAGE:5271111.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	82851075	82851075	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:82851075delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	83313227	83313227	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:83313227delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	83759202	83759202	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:83759202delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	84007892	84007892	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:84007892delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	84748612	84748613	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:84748612_84748613delAA	uc003dqi.2	-											Homo sapiens cDNA clone IMAGE:4824471.																														---	---	---	---
CADM2	253559	broad.mit.edu	37	3	85494745	85494745	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85494745delT	uc003dqj.2	+						CADM2_uc003dqk.2_Intron	NM_153184	NP_694854			immunoglobulin superfamily, member 4D						adherens junction organization|cell junction assembly	integral to membrane|plasma membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	86530946	86530946	+	IGR	DEL	C	-	-	rs148406060		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:86530946delC								CADM2 (412998 upstream) : VGLL3 (456179 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	86546759	86546760	+	IGR	INS	-	A	A	rs145122715	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:86546759_86546760insA								CADM2 (428811 upstream) : VGLL3 (440365 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	86714963	86714963	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:86714963delT								CADM2 (597015 upstream) : VGLL3 (272162 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	87446127	87446127	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87446127delA								POU1F1 (120390 upstream) : HTR1F (585599 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	87504550	87504550	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87504550delT								POU1F1 (178813 upstream) : HTR1F (527176 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	87599619	87599619	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87599619delA								POU1F1 (273882 upstream) : HTR1F (432107 downstream)																																			---	---	---	---
CGGBP1	8545	broad.mit.edu	37	3	88104473	88104473	+	3'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:88104473delT	uc003dqs.2	-	4					CGGBP1_uc003dqt.2_3'UTR|CGGBP1_uc003dqu.2_3'UTR	NM_001008390	NP_001008391			CGG triplet repeat binding protein 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	double-stranded DNA binding				0		Lung NSC(201;0.0283)		LUSC - Lung squamous cell carcinoma(29;0.00359)|Lung(72;0.00677)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	89031082	89031082	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89031082delA								C3orf38 (823969 upstream) : EPHA3 (125592 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	89629289	89629289	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89629289delT								EPHA3 (98007 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	90056125	90056125	+	IGR	DEL	T	-	-	rs73153370	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:90056125delT								EPHA3 (524843 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	90465482	90465482	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:90465482delA								EPHA3 (934200 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	93930490	93930490	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93930490delG								NSUN3 (84860 upstream) : LOC255025 (726617 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	93981183	93981184	+	IGR	DEL	TA	-	-	rs74407983	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93981183_93981184delTA								NSUN3 (135553 upstream) : LOC255025 (675923 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	94169563	94169563	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:94169563delT								NSUN3 (323933 upstream) : LOC255025 (487544 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	94946579	94946580	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:94946579_94946580delAC								LOC255025 (51500 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	95490806	95490807	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95490806_95490807delTG								LOC255025 (595727 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	95855347	95855348	+	IGR	INS	-	TG	TG	rs138099010	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95855347_95855348insTG								LOC255025 (960268 upstream) : EPHA6 (678077 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	95980542	95980542	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95980542delA								None (None upstream) : EPHA6 (552883 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	96286289	96286289	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96286289delT								None (None upstream) : EPHA6 (247136 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	96449259	96449259	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96449259delA								None (None upstream) : EPHA6 (84166 downstream)																																			---	---	---	---
EPHA6	285220	broad.mit.edu	37	3	97138467	97138468	+	Intron	INS	-	CA	CA	rs113526453		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97138467_97138468insCA	uc010how.1	+							NM_001080448	NP_001073917			EPH receptor A6 isoform a							integral to plasma membrane	ATP binding|ephrin receptor activity			stomach(5)|lung(4)|central_nervous_system(3)|breast(1)|skin(1)|ovary(1)|kidney(1)	16																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	98031434	98031434	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98031434delA								OR5H2 (28758 upstream) : OR5K4 (41264 downstream)																																			---	---	---	---
OR5K2	402135	broad.mit.edu	37	3	98215318	98215318	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98215318delT	uc011bgx.1	+							NM_001004737	NP_001004737			olfactory receptor, family 5, subfamily K,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2																		---	---	---	---
CPOX	1371	broad.mit.edu	37	3	98300982	98300983	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98300982_98300983delTT	uc003dsx.2	-							NM_000097	NP_000088			coproporphyrinogen oxidase precursor							mitochondrial intermembrane space	coproporphyrinogen oxidase activity|protein homodimerization activity				0																		---	---	---	---
ST3GAL6	10402	broad.mit.edu	37	3	98503990	98503990	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98503990delT	uc003dsz.2	+						ST3GAL6_uc003dsy.2_Intron|ST3GAL6_uc003dta.2_Intron|ST3GAL6_uc003dtb.2_Intron|ST3GAL6_uc003dtc.2_Intron|ST3GAL6_uc010hpd.2_Intron	NM_006100	NP_006091			alpha2,3-sialyltransferase VI						amino sugar metabolic process|glycolipid metabolic process|protein glycosylation|protein lipoylation	integral to Golgi membrane	sialyltransferase activity			ovary(1)	1																		---	---	---	---
FILIP1L	11259	broad.mit.edu	37	3	99794410	99794410	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99794410delT	uc003dtm.2	-						C3orf26_uc003dtl.2_Intron|FILIP1L_uc003dto.2_Intron	NM_182909	NP_878913			filamin A interacting protein 1-like isoform 1							cytoplasm|membrane|myosin complex|nucleus				ovary(1)	1																		---	---	---	---
C3orf26	84319	broad.mit.edu	37	3	99897121	99897121	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99897121delT	uc003dtl.2	+							NM_032359	NP_115735			hypothetical protein LOC84319								ATP binding|ATP-dependent helicase activity|nucleic acid binding			skin(1)	1																		---	---	---	---
LNP1	348801	broad.mit.edu	37	3	100121588	100121588	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100121588delT	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																		---	---	---	---
GPR128	84873	broad.mit.edu	37	3	100392269	100392269	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100392269delT	uc003duc.2	+						GPR128_uc011bhc.1_Intron|GPR128_uc003dud.2_Intron	NM_032787	NP_116176			G protein-coupled receptor 128 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)|skin(1)	4																		---	---	---	---
TFG	10342	broad.mit.edu	37	3	100465354	100465354	+	Intron	DEL	A	-	-	rs9811997	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100465354delA	uc003due.2	+						TFG_uc003duf.2_Intron|TFG_uc003dug.2_Intron|TFG_uc003duh.2_Intron|TFG_uc003dui.2_Intron	NM_006070	NP_006061			TRK-fused						positive regulation of I-kappaB kinase/NF-kappaB cascade	cytoplasm	signal transducer activity		TFG/ALK(7)	haematopoietic_and_lymphoid_tissue(7)|lung(2)|large_intestine(1)|prostate(1)	11								T	NTRK1|ALK	papillary thyroid|ALCL|NSCLC								---	---	---	---
ABI3BP	25890	broad.mit.edu	37	3	100531732	100531732	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100531732delT	uc003dun.2	-						ABI3BP_uc003duj.2_Intron|ABI3BP_uc003duk.2_Intron|ABI3BP_uc003dul.2_Intron|ABI3BP_uc011bhd.1_Intron|ABI3BP_uc003dum.2_Intron	NM_015429	NP_056244			ABI gene family, member 3 (NESH) binding protein							extracellular space				ovary(2)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	100741808	100741809	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100741808_100741809insT								ABI3BP (29474 upstream) : IMPG2 (203479 downstream)																																			---	---	---	---
SENP7	57337	broad.mit.edu	37	3	101197827	101197828	+	Intron	DEL	AT	-	-	rs9851641	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101197827_101197828delAT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	101435428	101435428	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101435428delA								LOC285359 (3169 upstream) : CEP97 (8066 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	102722817	102722817	+	IGR	DEL	T	-	-	rs75216373		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102722817delT								ZPLD1 (524132 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	102773786	102773787	+	IGR	DEL	TT	-	-	rs75325929		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102773786_102773787delTT								ZPLD1 (575101 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	103018000	103018000	+	IGR	DEL	T	-	-	rs67874551		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103018000delT								ZPLD1 (819315 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	103033046	103033046	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103033046delA								ZPLD1 (834361 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	103466599	103466599	+	IGR	DEL	C	-	-	rs11287237		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103466599delC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	104199626	104199626	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:104199626delA								None (None upstream) : ALCAM (886087 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	104301106	104301106	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:104301106delA								None (None upstream) : ALCAM (784607 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	104382369	104382369	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:104382369delT								None (None upstream) : ALCAM (703344 downstream)																																			---	---	---	---
ALCAM	214	broad.mit.edu	37	3	105295464	105295464	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105295464delA	uc003dvx.2	+	16					ALCAM_uc003dvy.2_3'UTR|ALCAM_uc010hpp.2_3'UTR|ALCAM_uc003dvz.2_3'UTR	NM_001627	NP_001618			activated leukocyte cell adhesion molecule						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(2)|breast(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	105316470	105316471	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105316470_105316471delTT								ALCAM (20727 upstream) : CBLB (60639 downstream)																																			---	---	---	---
CBLB	868	broad.mit.edu	37	3	105535737	105535737	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105535737delA	uc003dwc.2	-						CBLB_uc011bhi.1_Intron|CBLB_uc003dwd.1_Intron|CBLB_uc003dwe.1_Intron|CBLB_uc011bhj.1_Intron	NM_170662	NP_733762			Cas-Br-M (murine) ecotropic retroviral						cell surface receptor linked signaling pathway|NLS-bearing substrate import into nucleus	cytoplasm|nucleus	calcium ion binding|ligase activity|signal transducer activity|zinc ion binding			lung(4)|ovary(3)|breast(1)|skin(1)	9								Mis S		AML								---	---	---	---
Unknown	0	broad.mit.edu	37	3	105759051	105759051	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105759051delT								CBLB (170785 upstream) : LOC100302640 (796609 downstream)																																			---	---	---	---
LOC100302640	100302640	broad.mit.edu	37	3	106826276	106826276	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106826276delT	uc003dwf.3	-											Homo sapiens cDNA clone IMAGE:5284861.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	108001616	108001616	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108001616delT								IFT57 (60199 upstream) : HHLA2 (13777 downstream)																																			---	---	---	---
DZIP3	9666	broad.mit.edu	37	3	108349404	108349404	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108349404delT	uc003dxd.2	+						DZIP3_uc003dxf.1_Intron|DZIP3_uc011bhm.1_Intron|DZIP3_uc003dxe.1_Intron	NM_014648	NP_055463			DAZ interacting protein 3, zinc finger						protein polyubiquitination	cytoplasm	polyubiquitin binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	108507704	108507705	+	IGR	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108507704_108507705delAG								RETNLB (31574 upstream) : TRAT1 (33926 downstream)																																			---	---	---	---
GUCA1C	9626	broad.mit.edu	37	3	108644934	108644934	+	Intron	DEL	A	-	-	rs112360172		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108644934delA	uc003dxj.2	-						GUCA1C_uc003dxk.2_Intron	NM_005459	NP_005450			guanylate cyclase activator 1C						signal transduction|visual perception		calcium ion binding|calcium sensitive guanylate cyclase activator activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	108983357	108983365	+	IGR	DEL	GGAAGGAAG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108983357_108983365delGGAAGGAAG								C3orf66 (79250 upstream) : DPPA2 (29271 downstream)																																			---	---	---	---
FLJ25363	401082	broad.mit.edu	37	3	109168381	109168381	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109168381delT	uc003dxr.1	+							NM_001145553	NP_001139025			hypothetical protein LOC401082												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	110029543	110029543	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:110029543delA								FLJ25363 (815529 upstream) : PVRL3 (761322 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	110137054	110137054	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:110137054delA								FLJ25363 (923040 upstream) : PVRL3 (653811 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	110401054	110401054	+	IGR	DEL	T	-	-	rs113398685		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:110401054delT								None (None upstream) : PVRL3 (389811 downstream)																																			---	---	---	---
PLCXD2	257068	broad.mit.edu	37	3	111395998	111395998	+	Intron	DEL	A	-	-	rs140593925		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111395998delA	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																		---	---	---	---
TMPRSS7	344805	broad.mit.edu	37	3	111794490	111794490	+	Intron	DEL	T	-	-	rs112959291		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111794490delT	uc010hqb.2	+						TMPRSS7_uc011bhr.1_Intron	NM_001042575	NP_001036040			transmembrane protease, serine 7						proteolysis	integral to membrane|plasma membrane	serine-type endopeptidase activity			ovary(1)|kidney(1)	2																		---	---	---	---
ATG3	64422	broad.mit.edu	37	3	112267492	112267492	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112267492delA	uc003dzd.2	-						ATG3_uc003dzc.2_Intron|ATG3_uc010hqe.2_Intron	NM_022488	NP_071933			Apg3p						autophagic vacuole assembly|mitochondrial fragmentation involved in apoptosis|protein targeting to membrane|protein ubiquitination	cytoplasmic ubiquitin ligase complex|cytosol	Atg12 ligase activity|Atg8 ligase activity|enzyme binding			ovary(3)	3																		---	---	---	---
C3orf17	25871	broad.mit.edu	37	3	112736131	112736131	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112736131delA	uc003dzr.2	-						C3orf17_uc011bhz.1_Intron|C3orf17_uc010hqh.2_Intron|C3orf17_uc003dzt.2_Intron|C3orf17_uc003dzs.2_Intron|C3orf17_uc010hqg.2_Intron|C3orf17_uc011bia.1_Intron|C3orf17_uc003dzu.2_Intron|C3orf17_uc011bib.1_Intron|C3orf17_uc011bic.1_Intron|C3orf17_uc011bid.1_Intron	NM_015412	NP_056227			hypothetical protein LOC25871							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	112840292	112840293	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112840292_112840293delTT								C3orf17 (101737 upstream) : BOC (90119 downstream)																																			---	---	---	---
CCDC52	152185	broad.mit.edu	37	3	113219260	113219260	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113219260delT	uc003eag.3	-						CCDC52_uc003eaf.3_Intron|CCDC52_uc011bie.1_Intron|CCDC52_uc003eai.1_Intron	NM_144718	NP_653319			coiled-coil domain containing 52						cell division|mitosis	centriole|spindle	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	113241126	113241129	+	IGR	DEL	TGTG	-	-	rs111359167		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113241126_113241129delTGTG								CCDC52 (7092 upstream) : SIDT1 (10089 downstream)																																			---	---	---	---
GRAMD1C	54762	broad.mit.edu	37	3	113569031	113569031	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113569031delT	uc003eaq.3	+						GRAMD1C_uc011bil.1_Intron|GRAMD1C_uc011bim.1_Intron	NM_017577	NP_060047			GRAM domain containing 1C							integral to membrane				ovary(2)|skin(1)	3																		---	---	---	---
GRAMD1C	54762	broad.mit.edu	37	3	113663657	113663657	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113663657delA	uc003eaq.3	+						GRAMD1C_uc011bil.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																		---	---	---	---
ZBTB20	26137	broad.mit.edu	37	3	114120041	114120041	+	Intron	DEL	T	-	-	rs63534560		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114120041delT	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	114416352	114416352	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114416352delA	uc003ebk.2	-						ZBTB20_uc003ebl.2_Intron|ZBTB20_uc003ebm.2_Intron|ZBTB20_uc003ebn.2_Intron|ZBTB20_uc003ebp.2_Intron	NM_015642	NP_056457			zinc finger and BTB domain containing 20 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	115466923	115466923	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115466923delA								GAP43 (26589 upstream) : LSAMP (54299 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	115493479	115493479	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115493479delT								GAP43 (53145 upstream) : LSAMP (27743 downstream)																																			---	---	---	---
LSAMP	4045	broad.mit.edu	37	3	115721178	115721179	+	Intron	INS	-	A	A	rs113984501		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115721178_115721179insA	uc003ebt.2	-						LSAMP_uc011bis.1_Intron	NM_002338	NP_002329			limbic system-associated membrane protein						cell adhesion|nervous system development	anchored to membrane|plasma membrane					0		all_cancers(1;0.00189)|all_epithelial(1;0.0366)|Myeloproliferative disorder(1037;0.17)|all_neural(597;0.208)|Lung NSC(201;0.215)		GBM - Glioblastoma multiforme(114;0.00117)|LUSC - Lung squamous cell carcinoma(41;0.0407)|Lung(219;0.152)														---	---	---	---
LSAMP	4045	broad.mit.edu	37	3	115844239	115844239	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115844239delT	uc003ebt.2	-						LSAMP_uc011bis.1_Intron	NM_002338	NP_002329			limbic system-associated membrane protein						cell adhesion|nervous system development	anchored to membrane|plasma membrane					0		all_cancers(1;0.00189)|all_epithelial(1;0.0366)|Myeloproliferative disorder(1037;0.17)|all_neural(597;0.208)|Lung NSC(201;0.215)		GBM - Glioblastoma multiforme(114;0.00117)|LUSC - Lung squamous cell carcinoma(41;0.0407)|Lung(219;0.152)														---	---	---	---
LSAMP	4045	broad.mit.edu	37	3	115916238	115916238	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115916238delT	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	116343422	116343422	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116343422delT								LSAMP (819404 upstream) : LOC285194 (85213 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	116357355	116357355	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116357355delT								LSAMP (833337 upstream) : LOC285194 (71280 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	116683479	116683480	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116683479_116683480delAA								LOC285194 (247594 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	117271070	117271071	+	IGR	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117271070_117271071delCT								LOC285194 (835185 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	117883599	117883599	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117883599delA								None (None upstream) : IGSF11 (735882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	118122138	118122138	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118122138delT								None (None upstream) : IGSF11 (497343 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	118537734	118537734	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118537734delG								None (None upstream) : IGSF11 (81747 downstream)																																			---	---	---	---
ARHGAP31	57514	broad.mit.edu	37	3	119087144	119087145	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119087144_119087145insA	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																		---	---	---	---
GSK3B	2932	broad.mit.edu	37	3	119753940	119753940	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119753940delA	uc003edo.2	-						GSK3B_uc003edn.2_Intron	NM_001146156	NP_001139628			glycogen synthase kinase 3 beta isoform 2						axon guidance|epithelial to mesenchymal transition|ER overload response|glycogen metabolic process|hippocampus development|negative regulation of apoptosis|negative regulation of protein binding|negative regulation of protein complex assembly|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|positive regulation of cell-matrix adhesion|positive regulation of protein complex assembly|positive regulation of protein export from nucleus|positive regulation of Rac GTPase activity|regulation of microtubule-based process|superior temporal gyrus development	Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|nucleus|plasma membrane	ATP binding|beta-catenin binding|NF-kappaB binding|p53 binding|protein kinase A catalytic subunit binding|protein serine/threonine kinase activity|RNA polymerase II transcription factor binding|tau-protein kinase activity|ubiquitin protein ligase binding			lung(2)	2				GBM - Glioblastoma multiforme(114;0.24)	Lithium(DB01356)													---	---	---	---
STXBP5L	9515	broad.mit.edu	37	3	121085652	121085652	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121085652delT	uc003eec.3	+						STXBP5L_uc011bji.1_Intron	NM_014980	NP_055795			syntaxin binding protein 5-like						exocytosis|protein transport	cytoplasm|integral to membrane|plasma membrane				ovary(7)|skin(2)	9				GBM - Glioblastoma multiforme(114;0.0694)														---	---	---	---
FBXO40	51725	broad.mit.edu	37	3	121343727	121343727	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121343727delA	uc003eeg.2	+							NM_016298	NP_057382			F-box protein 40						muscle cell differentiation	centrosome|nucleus	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5				GBM - Glioblastoma multiforme(114;0.189)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	121754098	121754098	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121754098delA								ILDR1 (13068 upstream) : CD86 (20123 downstream)																																			---	---	---	---
KPNA1	3836	broad.mit.edu	37	3	122180188	122180188	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122180188delA	uc003efd.1	-						KPNA1_uc003efb.1_5'Flank|KPNA1_uc003efc.1_5'Flank|KPNA1_uc011bjr.1_Intron|KPNA1_uc010hrh.2_Intron|KPNA1_uc003efe.2_Intron	NM_002264	NP_002255			karyopherin alpha 1						DNA fragmentation involved in apoptotic nuclear change|NLS-bearing substrate import into nucleus|regulation of DNA recombination|viral genome transport in host cell|viral infectious cycle	cytosol|nuclear pore|nucleoplasm	nuclear localization sequence binding|protein binding|protein transporter activity				0				GBM - Glioblastoma multiforme(114;0.0898)														---	---	---	---
PARP14	54625	broad.mit.edu	37	3	122414253	122414253	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122414253delT	uc003efq.3	+						PARP14_uc010hrk.2_5'Flank	NM_017554	NP_060024			poly (ADP-ribose) polymerase family, member 14						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	NAD+ ADP-ribosyltransferase activity			ovary(2)|breast(2)|lung(1)|pancreas(1)	6				GBM - Glioblastoma multiforme(114;0.0531)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	122618929	122618929	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122618929delA								LOC100129550 (7667 upstream) : SEMA5B (9114 downstream)																																			---	---	---	---
PDIA5	10954	broad.mit.edu	37	3	122825581	122825581	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122825581delT	uc003egc.1	+						PDIA5_uc003egd.1_Intron	NM_006810	NP_006801			protein disulfide isomerase A5 precursor						cell redox homeostasis|glycerol ether metabolic process|protein folding|response to stress	endoplasmic reticulum lumen	electron carrier activity|protein disulfide isomerase activity|protein disulfide oxidoreductase activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.0427)														---	---	---	---
PTPLB	201562	broad.mit.edu	37	3	123263767	123263767	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123263767delA	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	123476899	123476900	+	Intron	INS	-	A	A	rs113861838		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123476899_123476900insA	uc003ego.2	-						MYLK_uc011bjw.1_Intron|MYLK_uc003egp.2_Intron|MYLK_uc003egq.2_Intron|MYLK_uc003egr.2_Intron|MYLK_uc003egs.2_Intron|MYLK_uc010hrs.1_Intron|MYLK_uc003egu.1_Intron	NM_053025	NP_444253			myosin light chain kinase isoform 1						aorta smooth muscle tissue morphogenesis|muscle contraction	cytosol	actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity			ovary(6)|skin(2)|stomach(1)	9		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)														---	---	---	---
MYLK	4638	broad.mit.edu	37	3	123559769	123559770	+	Intron	DEL	AA	-	-	rs67943701		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123559769_123559770delAA	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	124181595	124181595	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124181595delG	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																		---	---	---	---
SLC12A8	84561	broad.mit.edu	37	3	124823665	124823665	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124823665delT	uc003ehv.3	-						SLC12A8_uc003ehw.3_Intron|SLC12A8_uc003eht.3_Intron|SLC12A8_uc003ehu.3_Intron|SLC12A8_uc010hry.2_Intron	NM_024628	NP_078904			solute carrier family 12, member 8						potassium ion transport	integral to membrane	symporter activity				0																		---	---	---	---
ZNF148	7707	broad.mit.edu	37	3	124986105	124986105	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124986105delA	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	125044319	125044319	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125044319delT	uc003ehx.3	-						ZNF148_uc003ehz.3_Intron|ZNF148_uc010hsa.2_Intron|ZNF148_uc003eia.3_Intron|ZNF148_uc003ehy.2_Intron	NM_021964	NP_068799			zinc finger protein 148						cellular defense response|negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	Golgi apparatus|nucleus	protein binding|sequence-specific DNA binding|zinc ion binding			skin(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
SNX4	8723	broad.mit.edu	37	3	125192268	125192268	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125192268delT	uc003eib.2	-						SNX4_uc011bkf.1_Intron	NM_003794	NP_003785			sorting nexin 4						cell communication|endocytic recycling|endocytosis|protein transport	cytoplasmic dynein complex|early endosome membrane	phosphatidylinositol binding|protein binding			breast(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
SLC41A3	54946	broad.mit.edu	37	3	125782855	125782855	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125782855delG	uc003eij.2	-						SLC41A3_uc003eil.2_Intron|SLC41A3_uc003eik.2_Intron|SLC41A3_uc011bkh.1_Intron|SLC41A3_uc010hsd.1_Intron	NM_001008485	NP_001008485			solute carrier family 41, member 3 isoform 1							integral to membrane|plasma membrane	cation transmembrane transporter activity				0				GBM - Glioblastoma multiforme(114;0.167)														---	---	---	---
RPN1	6184	broad.mit.edu	37	3	128363639	128363639	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128363639delA	uc003ekr.1	-						RPN1_uc011bkq.1_Intron	NM_002950	NP_002941			ribophorin I precursor						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|melanosome|oligosaccharyltransferase complex|rough microsome	dolichyl-diphosphooligosaccharide-protein glycotransferase activity|protein binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(114;0.189)				T	EVI1	AML								---	---	---	---
RAB7A	7879	broad.mit.edu	37	3	128495112	128495112	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128495112delT	uc003eks.1	+						RAB7A_uc010hsv.1_Intron	NM_004637	NP_004628			RAB7, member RAS oncogene family						endocytosis|endosome to lysosome transport|epidermal growth factor catabolic process|protein transport|small GTPase mediated signal transduction	Golgi apparatus|late endosome|lysosome|melanosome|phagocytic vesicle	GDP binding|GTP binding|GTPase activity|protein binding				0				GBM - Glioblastoma multiforme(114;0.231)														---	---	---	---
KIAA1257	57501	broad.mit.edu	37	3	128666750	128666750	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128666750delA	uc003elh.1	-						KIAA1257_uc003elg.1_Intron					RecName: Full=Uncharacterized protein FLJ43738;												0																		---	---	---	---
KIAA1257	57501	broad.mit.edu	37	3	128697246	128697246	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128697246delA	uc003elj.3	-						KIAA1257_uc003elg.1_Intron|KIAA1257_uc003eli.3_Intron	NM_020741	NP_065792			hypothetical protein LOC57501												0																		---	---	---	---
KIAA1257	57501	broad.mit.edu	37	3	128706009	128706009	+	Intron	DEL	A	-	-	rs79108329		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128706009delA	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	129028192	129028192	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129028192delT								C3orf37 (4059 upstream) : H1FX (5423 downstream)																																			---	---	---	---
MBD4	8930	broad.mit.edu	37	3	129157777	129157777	+	Intron	DEL	A	-	-	rs76893037		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129157777delA	uc003emh.1	-						IFT122_uc003eml.2_5'Flank|IFT122_uc003emm.2_5'Flank|IFT122_uc003emn.2_5'Flank|IFT122_uc003emo.2_5'Flank|IFT122_uc003emp.2_5'Flank|IFT122_uc010htc.2_5'Flank|IFT122_uc011bky.1_5'Flank|IFT122_uc003emq.2_5'Flank|MBD4_uc003emi.1_Intron|MBD4_uc003emj.1_Intron|MBD4_uc003emk.1_Intron|MBD4_uc011bkw.1_Intron|IFT122_uc011bkx.1_5'Flank	NM_003925	NP_003916			methyl-CpG binding domain protein 4						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	130293993	130293993	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130293993delA	uc010htl.2	+							NM_001102608	NP_001096078			collagen type VI alpha 6 precursor						axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8																		---	---	---	---
COL6A6	131873	broad.mit.edu	37	3	130367861	130367861	+	Intron	DEL	T	-	-	rs72391450		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130367861delT	uc010htl.2	+						COL6A6_uc003eni.3_Intron	NM_001102608	NP_001096078			collagen type VI alpha 6 precursor						axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	130547277	130547277	+	IGR	DEL	A	-	-	rs3211035		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130547277delA								PIK3R4 (81581 upstream) : ATP2C1 (22168 downstream)																																			---	---	---	---
ATP2C1	27032	broad.mit.edu	37	3	130589015	130589015	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130589015delA	uc011bli.1	+						ATP2C1_uc011blg.1_Intron|ATP2C1_uc011blh.1_Intron	NM_001001487	NP_001001487			calcium-transporting ATPase 2C1 isoform 1b						actin cytoskeleton reorganization|ATP biosynthetic process|calcium-dependent cell-cell adhesion|cellular calcium ion homeostasis|cellular manganese ion homeostasis|epidermis development|Golgi calcium ion homeostasis|Golgi calcium ion transport|positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi apparatus|Golgi membrane|integral to membrane|trans-Golgi network	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|manganese ion binding|manganese-transporting ATPase activity|metal ion binding|signal transducer activity			skin(1)	1					Arsenic trioxide(DB01169)|Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Miconazole(DB01110)|Sevoflurane(DB01236)									Hailey-Hailey_disease				---	---	---	---
ATP2C1	27032	broad.mit.edu	37	3	130642992	130642992	+	Intron	DEL	T	-	-	rs143785164		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130642992delT	uc003enl.2	+						ATP2C1_uc011blg.1_Intron|ATP2C1_uc011blh.1_Intron|ATP2C1_uc011bli.1_Intron|ATP2C1_uc003enk.2_Intron|ATP2C1_uc003enm.2_Intron|ATP2C1_uc003enn.2_Intron|ATP2C1_uc003eno.2_Intron|ATP2C1_uc003enp.2_Intron|ATP2C1_uc003enq.2_Intron|ATP2C1_uc003enr.2_Intron|ATP2C1_uc003ens.2_Intron|ATP2C1_uc003ent.2_Intron	NM_014382	NP_055197			calcium-transporting ATPase 2C1 isoform 1a						actin cytoskeleton reorganization|ATP biosynthetic process|calcium-dependent cell-cell adhesion|cellular calcium ion homeostasis|cellular manganese ion homeostasis|epidermis development|Golgi calcium ion homeostasis|Golgi calcium ion transport|positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi apparatus|Golgi membrane|integral to membrane|trans-Golgi network	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|manganese ion binding|manganese-transporting ATPase activity|metal ion binding|signal transducer activity			skin(1)	1					Arsenic trioxide(DB01169)|Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Miconazole(DB01110)|Sevoflurane(DB01236)									Hailey-Hailey_disease				---	---	---	---
ATP2C1	27032	broad.mit.edu	37	3	130711967	130711970	+	Intron	DEL	TTTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130711967_130711970delTTTT	uc003enl.2	+						ATP2C1_uc011blg.1_Intron|ATP2C1_uc011blh.1_Intron|ATP2C1_uc011bli.1_Intron|ATP2C1_uc003enk.2_Intron|ATP2C1_uc003enm.2_Intron|ATP2C1_uc003enn.2_Intron|ATP2C1_uc003eno.2_Intron|ATP2C1_uc003enp.2_Intron|ATP2C1_uc003enq.2_Intron|ATP2C1_uc003enr.2_Intron|ATP2C1_uc003ens.2_Intron|ATP2C1_uc003ent.2_Intron|ATP2C1_uc003enu.2_Intron	NM_014382	NP_055197			calcium-transporting ATPase 2C1 isoform 1a						actin cytoskeleton reorganization|ATP biosynthetic process|calcium-dependent cell-cell adhesion|cellular calcium ion homeostasis|cellular manganese ion homeostasis|epidermis development|Golgi calcium ion homeostasis|Golgi calcium ion transport|positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi apparatus|Golgi membrane|integral to membrane|trans-Golgi network	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|manganese ion binding|manganese-transporting ATPase activity|metal ion binding|signal transducer activity			skin(1)	1					Arsenic trioxide(DB01169)|Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Miconazole(DB01110)|Sevoflurane(DB01236)									Hailey-Hailey_disease				---	---	---	---
CPNE4	131034	broad.mit.edu	37	3	131470608	131470609	+	Intron	INS	-	TT	TT	rs140869194	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131470608_131470609insTT	uc003eok.2	-						CPNE4_uc011blq.1_Intron|CPNE4_uc003eol.2_Intron|CPNE4_uc003eom.2_Intron	NM_130808	NP_570720			copine IV											upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
ACPP	55	broad.mit.edu	37	3	132042015	132042015	+	Intron	DEL	A	-	-	rs71881183		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132042015delA	uc010htp.2	+						ACPP_uc003eon.3_Intron|ACPP_uc003eop.3_Intron	NM_001099	NP_001090			acid phosphatase, prostate short isoform							extracellular region|lysosomal membrane	5'-nucleotidase activity|acid phosphatase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	132687669	132687669	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132687669delT								NCRNA00119 (94619 upstream) : TMEM108 (69502 downstream)																																			---	---	---	---
KY	339855	broad.mit.edu	37	3	134369247	134369247	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134369247delC	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	135482941	135482941	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135482941delA								EPHB1 (503636 upstream) : PPP2R3A (201626 downstream)																																			---	---	---	---
PPP2R3A	5523	broad.mit.edu	37	3	135722518	135722518	+	Intron	DEL	A	-	-	rs78480126		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135722518delA	uc003eqv.1	+						PPP2R3A_uc011blz.1_Intron	NM_002718	NP_002709			protein phosphatase 2, regulatory subunit B'',						protein dephosphorylation	protein phosphatase type 2A complex	calcium ion binding|protein binding|protein phosphatase type 2A regulator activity			ovary(3)|pancreas(1)|lung(1)|breast(1)|skin(1)	7																		---	---	---	---
MSL2	55167	broad.mit.edu	37	3	135908564	135908565	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135908564_135908565delAA	uc003eqx.1	-						MSL2_uc011bmb.1_Intron	NM_018133	NP_060603			ring finger protein 184 isoform 1						histone H4-K16 acetylation	MSL complex	zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
PCCB	5096	broad.mit.edu	37	3	136012781	136012781	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136012781delT	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	136272882	136272882	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136272882delA	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																		---	---	---	---
STAG1	10274	broad.mit.edu	37	3	136400643	136400643	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136400643delA	uc003era.1	-						STAG1_uc003erb.1_Intron|STAG1_uc003erc.1_Intron|STAG1_uc010hua.1_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																		---	---	---	---
STAG1	10274	broad.mit.edu	37	3	136406520	136406520	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136406520delG	uc003era.1	-						STAG1_uc003erb.1_Intron|STAG1_uc003erc.1_Intron|STAG1_uc010hua.1_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	136515570	136515571	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136515570_136515571insT								STAG1 (44325 upstream) : TMEM22 (22290 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	137219025	137219025	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137219025delT								IL20RB (489105 upstream) : SOX14 (264554 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	137859808	137859808	+	IGR	DEL	A	-	-	rs112835658		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137859808delA								A4GNT (8579 upstream) : DBR1 (20045 downstream)																																			---	---	---	---
ARMC8	25852	broad.mit.edu	37	3	137946471	137946472	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137946471_137946472insT	uc003esa.1	+						ARMC8_uc003erw.2_Intron|ARMC8_uc003erx.2_Intron|ARMC8_uc003ery.2_Intron|ARMC8_uc003erz.2_Intron|ARMC8_uc011bmf.1_Intron|ARMC8_uc011bmg.1_Intron|ARMC8_uc011bmh.1_Intron|ARMC8_uc003esb.1_Intron	NM_015396	NP_056211			armadillo repeat containing 8 isoform 2								binding				0																		---	---	---	---
ARMC8	25852	broad.mit.edu	37	3	137993076	137993077	+	Intron	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137993076_137993077delTG	uc003esa.1	+						TXNDC6_uc003esd.1_Intron|TXNDC6_uc010huf.1_Intron|TXNDC6_uc003ese.1_Intron|ARMC8_uc011bmf.1_Intron|ARMC8_uc011bmg.1_Intron|ARMC8_uc011bmh.1_Intron|ARMC8_uc003esb.1_Intron|ARMC8_uc003esc.1_Intron|ARMC8_uc003esf.1_Intron	NM_015396	NP_056211			armadillo repeat containing 8 isoform 2								binding				0																		---	---	---	---
TXNDC6	347736	broad.mit.edu	37	3	138050828	138050828	+	5'Flank	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138050828delA	uc003esg.2	-						TXNDC6_uc003ese.1_5'Flank	NM_178130	NP_835231			thioredoxin domain containing 6						cell redox homeostasis|CTP biosynthetic process|GTP biosynthetic process|UTP biosynthetic process	cytoplasm|cytoskeleton	ATP binding|nucleoside diphosphate kinase activity			breast(3)|ovary(1)|pancreas(1)	5																		---	---	---	---
CLSTN2	64084	broad.mit.edu	37	3	140129780	140129781	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140129780_140129781insA	uc003etn.2	+						CLSTN2_uc003etm.2_Intron	NM_022131	NP_071414			calsyntenin 2 precursor						homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			skin(3)|large_intestine(2)|pancreas(1)|central_nervous_system(1)	7															HNSCC(16;0.037)			---	---	---	---
CLSTN2	64084	broad.mit.edu	37	3	140131032	140131032	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140131032delT	uc003etn.2	+						CLSTN2_uc003etm.2_Intron	NM_022131	NP_071414			calsyntenin 2 precursor						homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			skin(3)|large_intestine(2)|pancreas(1)|central_nervous_system(1)	7															HNSCC(16;0.037)			---	---	---	---
CLSTN2	64084	broad.mit.edu	37	3	140186051	140186051	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140186051delA	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	140293713	140293714	+	IGR	DEL	TG	-	-	rs113552764		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140293713_140293714delTG								CLSTN2 (6796 upstream) : TRIM42 (103167 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	140431880	140431880	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140431880delT								TRIM42 (11889 upstream) : SLC25A36 (228782 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	141442961	141442961	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141442961delA								RASA2 (111764 upstream) : RNF7 (14090 downstream)																																			---	---	---	---
GK5	256356	broad.mit.edu	37	3	141932619	141932619	+	Intron	DEL	T	-	-	rs78127140	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141932619delT	uc003euq.1	-						GK5_uc010hus.1_Intron|GK5_uc010hut.1_Intron	NM_001039547	NP_001034636			glycerol kinase 5 (putative)						glycerol metabolic process		ATP binding|glycerol kinase activity				0																		---	---	---	---
XRN1	54464	broad.mit.edu	37	3	142142946	142142946	+	Intron	DEL	T	-	-	rs72184594		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142142946delT	uc003eus.2	-						XRN1_uc003eut.2_Intron|XRN1_uc003euu.2_Intron|XRN1_uc003euv.1_Intron|XRN1_uc003euw.2_Intron|XRN1_uc011bnh.1_Intron	NM_019001	NP_061874			5'-3' exoribonuclease 1 isoform a						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|histone mRNA catabolic process|nuclear mRNA surveillance|rRNA catabolic process	cytosol|Golgi apparatus|intermediate filament cytoskeleton|plasma membrane	5'-3' exonuclease activity|DNA binding|protein binding|RNA binding			ovary(3)	3																		---	---	---	---
ATR	545	broad.mit.edu	37	3	142201832	142201832	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142201832delT	uc003eux.3	-							NM_001184	NP_001175			ataxia telangiectasia and Rad3 related protein						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					---	---	---	---
Unknown	0	broad.mit.edu	37	3	142696261	142696261	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142696261delT								PAQR9 (14083 upstream) : SR140 (24111 downstream)																																			---	---	---	---
CHST2	9435	broad.mit.edu	37	3	142840376	142840376	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142840376delG	uc003evm.2	+	2	1607	c.718delG	c.(718-720)GGGfs	p.G240fs		NM_004267	NP_004258	Q9Y4C5	CHST2_HUMAN	carbohydrate (N-acetylglucosamine-6-O)	240	Lumenal (Potential).				inflammatory response|multicellular organismal development|N-acetylglucosamine metabolic process|sulfur compound metabolic process	integral to membrane|intrinsic to Golgi membrane|trans-Golgi network	N-acetylglucosamine 6-O-sulfotransferase activity			ovary(3)	3																		---	---	---	---
SLC9A9	285195	broad.mit.edu	37	3	142985838	142985839	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142985838_142985839delTT	uc003evn.2	-							NM_173653	NP_775924			solute carrier family 9 (sodium/hydrogen						regulation of pH	integral to membrane|late endosome membrane|recycling endosome	sodium:hydrogen antiporter activity			ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	143584076	143584076	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143584076delT								SLC9A9 (16730 upstream) : C3orf58 (106564 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	143976879	143976879	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143976879delA								C3orf58 (265670 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	144381184	144381185	+	IGR	INS	-	TG	TG	rs146336143	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144381184_144381185insTG								C3orf58 (669975 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	144487249	144487249	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144487249delT								C3orf58 (776040 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	145162573	145162573	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145162573delG								None (None upstream) : PLOD2 (624655 downstream)																																			---	---	---	---
PLSCR4	57088	broad.mit.edu	37	3	145924591	145924592	+	Intron	INS	-	T	T	rs150172444	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145924591_145924592insT	uc010huy.2	-						PLSCR4_uc010huz.2_Intron|PLSCR4_uc003evt.3_Intron|PLSCR4_uc010hva.2_Intron|PLSCR4_uc003evu.3_Intron	NM_001128305	NP_001121777			phospholipid scramblase 4 isoform a						blood coagulation|phospholipid scrambling	integral to membrane	calcium ion binding|phospholipid scramblase activity|SH3 domain binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	147088807	147088808	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147088807_147088808delTT								PLSCR5 (764804 upstream) : ZIC4 (15029 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	147156604	147156604	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147156604delT								ZIC1 (22100 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	148077926	148077926	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148077926delA								ZIC1 (943422 upstream) : AGTR1 (337732 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	148117179	148117179	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148117179delA								ZIC1 (982675 upstream) : AGTR1 (298479 downstream)																																			---	---	---	---
CP	1356	broad.mit.edu	37	3	148930106	148930107	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148930106_148930107insA	uc003ewy.3	-						CP_uc011bnr.1_Intron|CP_uc003ewx.3_5'Flank|CP_uc003ewz.2_Intron	NM_000096	NP_000087			ceruloplasmin precursor						cellular iron ion homeostasis|copper ion transport|transmembrane transport	extracellular space	chaperone binding|ferroxidase activity			ovary(1)	1		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	148943459	148943459	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148943459delA								CP (3627 upstream) : TM4SF18 (95397 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	149109996	149109998	+	IGR	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149109996_149109998delTTT								TM4SF1 (14428 upstream) : TM4SF4 (82436 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	150520220	150520220	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150520220delT								SIAH2 (38957 upstream) : CLRN1OS (50051 downstream)																																			---	---	---	---
CLRN1	7401	broad.mit.edu	37	3	150644691	150644691	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150644691delA	uc003eyk.1	-	3					CLRN1OS_uc011bny.1_Intron|CLRN1_uc003eyj.2_Intron	NM_174878	NP_777367			clarin 1 isoform a						equilibrioception|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	integral to membrane					0			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)															---	---	---	---
MED12L	116931	broad.mit.edu	37	3	150908389	150908389	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150908389delT	uc003eyp.2	+						MED12L_uc011bnz.1_Intron|MED12L_uc003eyn.2_Intron|MED12L_uc003eyo.2_Intron	NM_053002	NP_443728			mediator of RNA polymerase II transcription,						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	152465331	152465331	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152465331delT								MBNL1 (281763 upstream) : P2RY1 (87405 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	153158723	153158725	+	IGR	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153158723_153158725delAAA								RAP2B (272462 upstream) : C3orf79 (43559 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	153457211	153457212	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153457211_153457212delAC								C3orf79 (236728 upstream) : SGEF (381937 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	154268279	154268279	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154268279delT								GPR149 (120775 upstream) : MME (473634 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	154473576	154473576	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154473576delA								GPR149 (326072 upstream) : MME (268337 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	154526840	154526842	+	IGR	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154526840_154526842delTTT								GPR149 (379336 upstream) : MME (215071 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	155045515	155045515	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155045515delA								MME (143997 upstream) : PLCH1 (152156 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	155116835	155116835	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155116835delT								MME (215317 upstream) : PLCH1 (80836 downstream)																																			---	---	---	---
PLCH1	23007	broad.mit.edu	37	3	155215514	155215515	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155215514_155215515insT	uc011bok.1	-						PLCH1_uc011boj.1_Intron|PLCH1_uc011bol.1_Intron	NM_001130960	NP_001124432			phospholipase C eta 1 isoform a						lipid catabolic process|phosphatidylinositol-mediated signaling	membrane	calcium ion binding|calcium-dependent phospholipase C activity|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(3)|ovary(1)	4			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)															---	---	---	---
PLCH1	23007	broad.mit.edu	37	3	155386943	155386945	+	Intron	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155386943_155386945delAAA	uc011bok.1	-						PLCH1_uc011boj.1_Intron|PLCH1_uc011bol.1_Intron	NM_001130960	NP_001124432			phospholipase C eta 1 isoform a						lipid catabolic process|phosphatidylinositol-mediated signaling	membrane	calcium ion binding|calcium-dependent phospholipase C activity|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(3)|ovary(1)	4			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	155528799	155528799	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155528799delT								C3orf33 (4744 upstream) : SLC33A1 (15517 downstream)																																			---	---	---	---
SLC33A1	9197	broad.mit.edu	37	3	155545820	155545820	+	Intron	DEL	A	-	-	rs75665348		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155545820delA	uc003fan.3	-						SLC33A1_uc003fao.1_3'UTR	NM_004733	NP_004724			acetyl-coenzyme A transporter						cell death|transmembrane transport	endoplasmic reticulum membrane|Golgi membrane|integral to plasma membrane|membrane fraction	acetyl-CoA transporter activity			ovary(2)|large_intestine(1)|pancreas(1)	4			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)															---	---	---	---
GMPS	8833	broad.mit.edu	37	3	155624169	155624169	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155624169delT	uc003faq.2	+						GMPS_uc011bom.1_Intron	NM_003875	NP_003866			guanine monophosphate synthetase						glutamine metabolic process|purine base biosynthetic process	cytosol	ATP binding|GMP synthase (glutamine-hydrolyzing) activity|GMP synthase activity			ovary(2)|lung(1)	3			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)		L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)			T	MLL	AML								---	---	---	---
KCNAB1	7881	broad.mit.edu	37	3	156140687	156140687	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156140687delA	uc003far.2	+						KCNAB1_uc011bon.1_Intron|KCNAB1_uc003fas.2_Intron|KCNAB1_uc003fat.2_Intron|KCNAB1_uc010hvt.1_Intron	NM_172160	NP_751892			potassium voltage-gated channel, shaker-related							cytoplasm|integral to membrane	oxidoreductase activity|potassium channel regulator activity|voltage-gated potassium channel activity			ovary(3)|skin(1)	4			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	156358503	156358506	+	IGR	DEL	TTTG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156358503_156358506delTTTG								SSR3 (85568 upstream) : LOC100287227 (32458 downstream)																																			---	---	---	---
LEKR1	389170	broad.mit.edu	37	3	156707600	156707601	+	Intron	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156707600_156707601delCT	uc003fba.1	+							NM_001004316	NP_001004316			leucine, glutamate and lysine rich 1												0			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	156784786	156784786	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156784786delA								LEKR1 (20868 upstream) : CCNL1 (79511 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	156918196	156918196	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156918196delT								CCNL1 (39714 upstream) : VEPH1 (60502 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	157576756	157576756	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157576756delA								C3orf55 (257737 upstream) : SHOX2 (237045 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	158329610	158329610	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158329610delT								MLF1 (5358 upstream) : GFM1 (32707 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	158339703	158339703	+	IGR	DEL	C	-	-	rs4680447	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158339703delC								MLF1 (15451 upstream) : GFM1 (22614 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	158553223	158553226	+	IGR	DEL	AAAC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158553223_158553226delAAAC								MFSD1 (5719 upstream) : SCHIP1 (233891 downstream)																																			---	---	---	---
SCHIP1	29970	broad.mit.edu	37	3	159217777	159217778	+	Intron	DEL	TT	-	-	rs71687144		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159217777_159217778delTT	uc003fcs.1	+						SCHIP1_uc003fcq.1_Intron|SCHIP1_uc003fcr.1_Intron|SCHIP1_uc003fct.1_Intron	NM_014575	NP_055390			schwannomin interacting protein 1							cytoplasm	identical protein binding|protein binding			ovary(1)|central_nervous_system(1)	2			LUSC - Lung squamous cell carcinoma(72;0.00523)|Lung(72;0.00534)															---	---	---	---
IFT80	57560	broad.mit.edu	37	3	160067243	160067243	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160067243delA	uc011boy.1	-						IFT80_uc003fda.2_Intron|IFT80_uc003fdb.1_Intron|IFT80_uc003fdd.1_Intron|IFT80_uc003fde.1_Intron	NM_020800	NP_065851			WD repeat domain 56							cilium axoneme|microtubule basal body				ovary(1)	1			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)															---	---	---	---
PPM1L	151742	broad.mit.edu	37	3	160508485	160508485	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160508485delT	uc003fdr.2	+							NM_139245	NP_640338			protein phosphatase 1 (formerly 2C)-like						protein dephosphorylation|sphingolipid metabolic process	endoplasmic reticulum membrane|integral to membrane|protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity			breast(1)	1			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	161302578	161302578	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161302578delT								OTOL1 (80850 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	162024629	162024629	+	IGR	DEL	A	-	-	rs74334657		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162024629delA								OTOL1 (802901 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	162025163	162025163	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162025163delT								OTOL1 (803435 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	162395468	162395468	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162395468delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	163090254	163090254	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163090254delT								None (None upstream) : MIR1263 (799005 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	163244479	163244479	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163244479delA								None (None upstream) : MIR1263 (644780 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	164005800	164005800	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164005800delT								MIR1263 (116456 upstream) : MIR720 (53329 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	164519031	164519031	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164519031delT								MIR720 (459793 upstream) : SI (177656 downstream)																																			---	---	---	---
SI	6476	broad.mit.edu	37	3	164775490	164775491	+	Intron	INS	-	C	C	rs9878023	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164775490_164775491insC	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	165986287	165986287	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165986287delA								BCHE (431034 upstream) : ZBBX (971794 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	166307996	166307996	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166307996delA								BCHE (752743 upstream) : ZBBX (650085 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	168033025	168033025	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168033025delT								GOLIM4 (219608 upstream) : MIR551B (236617 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	168746036	168746036	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168746036delA								C3orf50 (197664 upstream) : MECOM (55251 downstream)																																			---	---	---	---
MECOM	2122	broad.mit.edu	37	3	168900672	168900672	+	Intron	DEL	A	-	-	rs139690912		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168900672delA	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	169201795	169201795	+	Intron	DEL	T	-	-	rs78338445		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169201795delT	uc011bpj.1	-						MECOM_uc011bpk.1_Intron|MECOM_uc010hwn.2_Intron|MECOM_uc011bpl.1_Intron	NM_004991	NP_004982			MDS1 and EVI1 complex locus isoform c						apoptosis|cell differentiation|hemopoietic stem cell proliferation|negative regulation of JNK cascade|negative regulation of programmed cell death|negative regulation of transcription, DNA-dependent|regulation of cell cycle	nuclear speck	DNA binding|protein binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(5)|skin(5)|upper_aerodigestive_tract(1)|central_nervous_system(1)|ovary(1)|pancreas(1)	14																		---	---	---	---
MECOM	2122	broad.mit.edu	37	3	169341583	169341584	+	Intron	DEL	AC	-	-	rs62295983		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169341583_169341584delAC	uc011bpj.1	-						MECOM_uc011bpk.1_Intron|MECOM_uc010hwn.2_Intron|MECOM_uc011bpl.1_Intron	NM_004991	NP_004982			MDS1 and EVI1 complex locus isoform c						apoptosis|cell differentiation|hemopoietic stem cell proliferation|negative regulation of JNK cascade|negative regulation of programmed cell death|negative regulation of transcription, DNA-dependent|regulation of cell cycle	nuclear speck	DNA binding|protein binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(5)|skin(5)|upper_aerodigestive_tract(1)|central_nervous_system(1)|ovary(1)|pancreas(1)	14																		---	---	---	---
MECOM	2122	broad.mit.edu	37	3	169360526	169360526	+	Intron	DEL	A	-	-	rs36037830		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169360526delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	169473182	169473183	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169473182_169473183delAC								MECOM (91619 upstream) : TERC (9215 downstream)																																			---	---	---	---
GPR160	26996	broad.mit.edu	37	3	169796604	169796604	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169796604delA	uc003fgi.2	+						GPR160_uc010hwq.2_Intron	NM_014373	NP_055188			G protein-coupled receptor 160							integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_cancers(22;3.26e-22)|all_epithelial(15;5.71e-27)|all_lung(20;8.41e-17)|Lung NSC(18;3.49e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)															---	---	---	---
PHC3	80012	broad.mit.edu	37	3	169860249	169860251	+	Intron	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169860249_169860251delAAA	uc010hws.1	-						PHC3_uc003fgl.2_Intron|PHC3_uc011bpq.1_Intron|PHC3_uc011bpr.1_Intron|PHC3_uc003fgm.2_Intron|uc003fgn.1_5'Flank	NM_024947	NP_079223			polyhomeotic like 3						multicellular organismal development	PcG protein complex	DNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)															---	---	---	---
PHC3	80012	broad.mit.edu	37	3	169895647	169895648	+	Intron	INS	-	G	G	rs141787685	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169895647_169895648insG	uc010hws.1	-						PHC3_uc003fgl.2_Intron|PHC3_uc011bpq.1_Intron|PHC3_uc011bpr.1_Intron|PHC3_uc003fgm.2_Intron|PHC3_uc003fgo.1_Intron|PHC3_uc003fgp.3_Intron|PHC3_uc003fgq.3_Intron	NM_024947	NP_079223			polyhomeotic like 3						multicellular organismal development	PcG protein complex	DNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	170118458	170118461	+	IGR	DEL	TTCT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170118458_170118461delTTCT								SKIL (7510 upstream) : CLDN11 (18192 downstream)																																			---	---	---	---
SLC7A14	57709	broad.mit.edu	37	3	170178474	170178475	+	3'UTR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170178474_170178475delAA	uc003fgz.2	-	8					CLDN11_uc011bpt.1_Intron	NM_020949	NP_066000			solute carrier family 7 (cationic amino acid							integral to membrane	amino acid transmembrane transporter activity			ovary(2)|upper_aerodigestive_tract(1)|liver(1)|central_nervous_system(1)	5	all_cancers(22;2.41e-22)|all_epithelial(15;4.2e-27)|all_lung(20;1.17e-16)|Lung NSC(18;4.91e-16)|Ovarian(172;0.000902)|Breast(254;0.137)		Lung(28;6.23e-13)|LUSC - Lung squamous cell carcinoma(14;1.48e-12)															---	---	---	---
SLC7A14	57709	broad.mit.edu	37	3	170193509	170193509	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170193509delT	uc003fgz.2	-						CLDN11_uc011bpt.1_Intron|uc003fha.1_Intron	NM_020949	NP_066000			solute carrier family 7 (cationic amino acid							integral to membrane	amino acid transmembrane transporter activity			ovary(2)|upper_aerodigestive_tract(1)|liver(1)|central_nervous_system(1)	5	all_cancers(22;2.41e-22)|all_epithelial(15;4.2e-27)|all_lung(20;1.17e-16)|Lung NSC(18;4.91e-16)|Ovarian(172;0.000902)|Breast(254;0.137)		Lung(28;6.23e-13)|LUSC - Lung squamous cell carcinoma(14;1.48e-12)															---	---	---	---
CLDN11	5010	broad.mit.edu	37	3	170414201	170414202	+	Intron	DEL	TT	-	-	rs71847330		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170414201_170414202delTT	uc011bpt.1	+						uc003fha.1_Intron	NM_005602	NP_005593			claudin 11						calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity			central_nervous_system(1)	1	all_cancers(22;5.62e-23)|all_epithelial(15;7.54e-28)|all_lung(20;2.51e-17)|Lung NSC(18;1.02e-16)|Ovarian(172;0.000567)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)															---	---	---	---
TNIK	23043	broad.mit.edu	37	3	170935341	170935341	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170935341delA	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)															---	---	---	---
SPATA16	83893	broad.mit.edu	37	3	172623935	172623935	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172623935delT	uc003fin.3	-							NM_031955	NP_114161			spermatogenesis associated 16						cell differentiation|multicellular organismal development|spermatogenesis	Golgi apparatus	binding			ovary(2)|skin(1)	3	Ovarian(172;0.00319)|Breast(254;0.197)		LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	172866705	172866706	+	IGR	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172866705_172866706delAG								SPATA16 (7673 upstream) : NLGN1 (249538 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	172962606	172962606	+	IGR	DEL	C	-	-	rs111654067		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172962606delC								SPATA16 (103574 upstream) : NLGN1 (153638 downstream)																																			---	---	---	---
NLGN1	22871	broad.mit.edu	37	3	173156137	173156137	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173156137delA	uc003fio.1	+							NM_014932	NP_055747			neuroligin 1						calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	174392300	174392301	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174392300_174392301delTT	uc003fir.2	+						uc003fis.2_Intron|uc010hwx.1_Intron					Homo sapiens NAALADL2 gene, partial 5'UTR, variant 1.																														---	---	---	---
NAALADL2	254827	broad.mit.edu	37	3	174991508	174991509	+	Intron	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174991508_174991509delTG	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	175833874	175833877	+	IGR	DEL	TTTT	-	-	rs79982935		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175833874_175833877delTTTT								NAALADL2 (310448 upstream) : TBL1XR1 (904666 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	176627077	176627078	+	IGR	INS	-	T	T	rs150043132	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176627077_176627078insT								None (None upstream) : TBL1XR1 (111465 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	177252923	177252925	+	IGR	DEL	CTA	-	-	rs149190985		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177252923_177252925delCTA								TBL1XR1 (337875 upstream) : None (None downstream)																																			---	---	---	---
ZMAT3	64393	broad.mit.edu	37	3	178755450	178755450	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178755450delA	uc003fjg.2	-						ZMAT3_uc010hxa.2_Intron|ZMAT3_uc003fji.2_Intron	NM_022470	NP_071915			p53 target zinc finger protein isoform 1						apoptosis|protein transport|regulation of growth|response to DNA damage stimulus|transmembrane transport	nucleolus	RNA binding|zinc ion binding			ovary(2)	2	all_cancers(143;3.31e-18)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;6.74e-27)|GBM - Glioblastoma multiforme(14;0.00448)|BRCA - Breast invasive adenocarcinoma(182;0.0527)															---	---	---	---
ZNF639	51193	broad.mit.edu	37	3	179050962	179050962	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179050962delA	uc003fjq.1	+						ZNF639_uc003fjr.1_Intron	NM_016331	NP_057415			zinc finger protein 639						initiation of viral infection|negative regulation by host of viral transcription|negative regulation of transcription, DNA-dependent|positive regulation by host of viral transcription|positive regulation of cell growth|positive regulation of transcription, DNA-dependent	nucleus	protein self-association|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding				0	all_cancers(143;7.9e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0923)															---	---	---	---
GNB4	59345	broad.mit.edu	37	3	179151493	179151493	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179151493delA	uc003fjv.3	-							NM_021629	NP_067642			guanine nucleotide-binding protein, beta-4						cellular response to glucagon stimulus|energy reserve metabolic process	plasma membrane	signal transducer activity			skin(2)	2	all_cancers(143;2.01e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.237)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	179212051	179212054	+	IGR	DEL	AAGA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179212051_179212054delAAGA								GNB4 (42680 upstream) : ACTL6A (68654 downstream)																																			---	---	---	---
USP13	8975	broad.mit.edu	37	3	179479203	179479203	+	Intron	DEL	T	-	-	rs74695249		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179479203delT	uc003fkh.2	+							NM_003940	NP_003931			ubiquitin thiolesterase 13						ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(1)	1	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)															---	---	---	---
PEX5L	51555	broad.mit.edu	37	3	179527486	179527486	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179527486delT	uc003fki.1	-						PEX5L_uc011bqd.1_Intron|PEX5L_uc011bqe.1_Intron|PEX5L_uc011bqf.1_Intron|PEX5L_uc003fkj.1_Intron|PEX5L_uc010hxd.1_Intron|PEX5L_uc011bqg.1_Intron|PEX5L_uc011bqh.1_Intron	NM_016559	NP_057643			peroxisomal biogenesis factor 5-like						protein import into peroxisome matrix|regulation of cAMP-mediated signaling	cytosol|peroxisomal membrane	peroxisome matrix targeting signal-1 binding			ovary(3)|large_intestine(1)	4	all_cancers(143;3.94e-14)|Ovarian(172;0.0338)|Breast(254;0.183)		OV - Ovarian serous cystadenocarcinoma(80;1.75e-26)|GBM - Glioblastoma multiforme(14;0.000518)															---	---	---	---
CCDC39	339829	broad.mit.edu	37	3	180371842	180371845	+	Intron	DEL	AAAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180371842_180371845delAAAA	uc010hxe.2	-						CCDC39_uc003fkn.2_Intron	NM_181426	NP_852091			coiled-coil domain containing 39						axonemal dynein complex assembly|ciliary cell motility|cilium movement involved in determination of left/right asymmetry|flagellar cell motility	cilium axoneme|cytoplasm|cytoskeleton				ovary(4)	4	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	180462992	180462992	+	Intron	DEL	T	-	-	rs33913797		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180462992delT	uc003fko.2	-											Homo sapiens mRNA; cDNA DKFZp434A128 (from clone DKFZp434A128).																														---	---	---	---
FXR1	8087	broad.mit.edu	37	3	180670364	180670364	+	Intron	DEL	A	-	-	rs36069943		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180670364delA	uc003fkq.2	+						FXR1_uc003fkp.2_Intron|FXR1_uc003fkr.2_Intron|FXR1_uc011bqj.1_Intron|FXR1_uc003fks.2_Intron|FXR1_uc011bqk.1_Intron|FXR1_uc011bql.1_Intron	NM_005087	NP_005078			fragile X mental retardation-related protein 1						apoptosis|cell differentiation|muscle organ development	nucleolus|polysome				breast(1)	1	all_cancers(143;6.07e-14)|Ovarian(172;0.0212)		Epithelial(37;3.05e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.4e-22)															---	---	---	---
SOX2	6657	broad.mit.edu	37	3	181431227	181431227	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181431227delA	uc003fkx.2	+	1					SOX2OT_uc003fkv.2_Intron|SOX2OT_uc003fkw.3_Intron	NM_003106	NP_003097			sex-determining region Y-box 2						cell cycle arrest|chromatin organization|eye development|glial cell fate commitment|inner ear development|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell proliferation|negative regulation of neuron differentiation|osteoblast differentiation|pituitary gland development|positive regulation of MAPKKK cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of caspase activity|response to growth factor stimulus|response to wounding|somatic stem cell maintenance	cytosol|transcription factor complex	miRNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding				0	all_cancers(143;1.22e-16)|Ovarian(172;0.0283)		all cancers(12;1.82e-48)|Epithelial(37;9.85e-40)|OV - Ovarian serous cystadenocarcinoma(80;7.37e-23)|Lung(8;2.01e-21)|GBM - Glioblastoma multiforme(1;2.13e-08)					A		NSCLC|oesophageal squamous carcinoma		MICROPHTHALMIA AND ESOPHAGEAL ATRESIA SYNDROME						---	---	---	---
Unknown	0	broad.mit.edu	37	3	181636721	181636721	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181636721delT								SOX2OT (177718 upstream) : ATP11B (874570 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	181729784	181729784	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181729784delT								SOX2OT (270781 upstream) : ATP11B (781507 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	181968812	181968813	+	IGR	INS	-	T	T	rs139086326	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181968812_181968813insT								SOX2OT (509809 upstream) : ATP11B (542478 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	182092195	182092195	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182092195delT								SOX2OT (633192 upstream) : ATP11B (419096 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	182102044	182102044	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182102044delA								SOX2OT (643041 upstream) : ATP11B (409247 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	182457006	182457007	+	IGR	INS	-	AG	AG	rs139333212	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182457006_182457007insAG								SOX2OT (998003 upstream) : ATP11B (54284 downstream)																																			---	---	---	---
MCCC1	56922	broad.mit.edu	37	3	182807402	182807402	+	Intron	DEL	A	-	-	rs75056919		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182807402delA	uc003fle.2	-						MCCC1_uc010hxi.2_Intron|MCCC1_uc011bqo.1_Intron|MCCC1_uc003flf.2_Intron|MCCC1_uc003flg.2_Intron|MCCC1_uc011bqp.1_Intron|MCCC1_uc011bqq.1_Intron	NM_020166	NP_064551			methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)						biotin metabolic process|leucine catabolic process	mitochondrial inner membrane|mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|metal ion binding|methylcrotonoyl-CoA carboxylase activity			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)													---	---	---	---
MCCC1	56922	broad.mit.edu	37	3	182835972	182835972	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182835972delT	uc003flg.2	-											RecName: Full=Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial;          Short=MCCase subunit alpha;          EC=6.4.1.4; AltName: Full=3-methylcrotonyl-CoA carboxylase 1; AltName: Full=3-methylcrotonyl-CoA:carbon dioxide ligase subunit alpha; AltName: Full=3-methylcrotonyl-CoA carboxylase biotin-containing subunit; Flags: Precursor;						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	183042523	183042523	+	Intron	DEL	A	-	-	rs147168829		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183042523delA	uc003fli.1	-						MCF2L2_uc003flj.1_Intron|MCF2L2_uc003flp.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)															---	---	---	---
MCF2L2	23101	broad.mit.edu	37	3	183084434	183084434	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183084434delA	uc003fli.1	-						MCF2L2_uc003flj.1_Intron|MCF2L2_uc003flp.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)															---	---	---	---
ABCC5	10057	broad.mit.edu	37	3	183677636	183677636	+	Intron	DEL	A	-	-	rs35912087		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183677636delA	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)															---	---	---	---
EHHADH	1962	broad.mit.edu	37	3	184958013	184958014	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184958013_184958014delTT	uc003fpf.2	-						EHHADH_uc011brs.1_Intron	NM_001966	NP_001957			enoyl-Coenzyme A, hydratase/3-hydroxyacyl							peroxisome	3-hydroxyacyl-CoA dehydrogenase activity|coenzyme binding|dodecenoyl-CoA delta-isomerase activity|enoyl-CoA hydratase activity			ovary(3)	3	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)		NADH(DB00157)													---	---	---	---
LIPH	200879	broad.mit.edu	37	3	185250285	185250285	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185250285delA	uc003fpm.2	-						LIPH_uc010hyh.2_Intron	NM_139248	NP_640341			lipase, member H precursor						lipid catabolic process	extracellular space|plasma membrane	heparin binding|phospholipase activity			ovary(1)|pancreas(1)	2	all_cancers(143;8.87e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)															---	---	---	---
SENP2	59343	broad.mit.edu	37	3	185322552	185322552	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185322552delT	uc003fpn.2	+						SENP2_uc011brv.1_Intron|SENP2_uc011brw.1_Intron	NM_021627	NP_067640			SUMO1/sentrin/SMT3 specific protease 2						mRNA transport|protein desumoylation|protein transport|proteolysis|regulation of Wnt receptor signaling pathway|transmembrane transport|Wnt receptor signaling pathway	cytoplasm|nuclear membrane|nuclear pore	protein binding|SUMO-specific protease activity				0	all_cancers(143;1.28e-10)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	186805498	186805499	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186805498_186805499delTT								ST6GAL1 (9159 upstream) : RPL39L (33242 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	186911598	186911599	+	IGR	INS	-	AC	AC			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186911598_186911599insAC								RPL39L (54335 upstream) : RTP1 (3675 downstream)																																			---	---	---	---
MASP1	5648	broad.mit.edu	37	3	186964879	186964880	+	Intron	INS	-	T	T	rs137929458	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186964879_186964880insT	uc003frh.1	-						MASP1_uc003fri.2_Intron|MASP1_uc003frj.2_Intron|MASP1_uc003frk.1_3'UTR|MASP1_uc011bse.1_3'UTR	NM_001879	NP_001870			mannan-binding lectin serine protease 1 isoform						complement activation, lectin pathway|negative regulation of complement activation|proteolysis	extracellular space	calcium ion binding|calcium-dependent protein binding|protein binding|protein homodimerization activity|serine-type endopeptidase activity			ovary(2)|breast(1)|liver(1)	4	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	187043032	187043032	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187043032delT								MASP1 (33280 upstream) : RTP4 (43136 downstream)																																			---	---	---	---
LPP	4026	broad.mit.edu	37	3	188202760	188202760	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188202760delT	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-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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								---	---	---	---
TP63	8626	broad.mit.edu	37	3	189475664	189475664	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189475664delA	uc003fry.2	+						TP63_uc003frx.2_Intron|TP63_uc003frz.2_Intron|TP63_uc010hzc.1_Intron	NM_003722	NP_003713			tumor protein p63 isoform 1						anti-apoptosis|cellular response to UV|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of transcription from RNA polymerase II promoter|Notch signaling pathway|positive regulation of Notch signaling pathway|protein homotetramerization|regulation of neuron apoptosis|response to gamma radiation|response to X-ray	chromatin|cytosol|dendrite|Golgi apparatus|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|metal ion binding|p53 binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(5)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	12	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)										Hay-Wells_syndrome	HNSCC(45;0.13)			---	---	---	---
LEPREL1	55214	broad.mit.edu	37	3	189813756	189813757	+	Intron	INS	-	CAA	CAA	rs139323041	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189813756_189813757insCAA	uc011bsk.1	-						LEPREL1_uc003fsg.2_Intron	NM_018192	NP_060662			leprecan-like 1 isoform a						collagen metabolic process|negative regulation of cell proliferation|peptidyl-proline hydroxylation	basement membrane|endoplasmic reticulum|Golgi apparatus	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 3-dioxygenase activity			breast(3)|ovary(1)	4	all_cancers(143;4.01e-10)|Ovarian(172;0.0925)		Lung(62;4.35e-05)	GBM - Glioblastoma multiforme(93;0.02)	L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	189861058	189861059	+	IGR	DEL	TT	-	-	rs112117085		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189861058_189861059delTT								LEPREL1 (20832 upstream) : CLDN1 (162444 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	189865623	189865623	+	IGR	DEL	G	-	-	rs145813785		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189865623delG								LEPREL1 (25397 upstream) : CLDN1 (157880 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	190195024	190195024	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190195024delA								TMEM207 (27359 upstream) : IL1RAP (36867 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	190789634	190789635	+	IGR	DEL	TC	-	-	rs35668954		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190789634_190789635delTC								SNAR-I (193795 upstream) : OSTN (140687 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	191295306	191295306	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191295306delT								PYDC2 (116063 upstream) : FGF12 (564378 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	191335470	191335470	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191335470delG								PYDC2 (156227 upstream) : FGF12 (524214 downstream)																																			---	---	---	---
FGF12	2257	broad.mit.edu	37	3	192078485	192078485	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192078485delT	uc003fsx.2	-						FGF12_uc003fsy.2_Intron	NM_021032	NP_066360			fibroblast growth factor 12 isoform 1						cell-cell signaling|heart development|JNK cascade|nervous system development|signal transduction	extracellular space|nucleus	growth factor activity|heparin binding			ovary(1)|skin(1)|lung(1)|pancreas(1)	4	all_cancers(143;1.72e-08)|Ovarian(172;0.0634)|Breast(254;0.247)	Lung NSC(153;0.21)	LUSC - Lung squamous cell carcinoma(58;5.45e-06)|Lung(62;6.17e-06)	GBM - Glioblastoma multiforme(46;0.00032)														---	---	---	---
FGF12	2257	broad.mit.edu	37	3	192147983	192147983	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192147983delA	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	192345641	192345642	+	Intron	INS	-	TG	TG	rs138709721	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192345641_192345642insTG	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	192664579	192664579	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192664579delT								C3orf59 (28629 upstream) : HRASLS (294339 downstream)																																			---	---	---	---
OPA1	4976	broad.mit.edu	37	3	193366428	193366428	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193366428delA	uc003ftm.2	+						OPA1_uc003ftg.2_Intron|OPA1_uc003fth.2_Intron|OPA1_uc003fti.2_Intron|OPA1_uc003ftj.2_Intron|OPA1_uc003ftk.2_Intron|OPA1_uc003ftl.2_Intron|OPA1_uc003ftn.2_Intron	NM_015560	NP_056375			optic atrophy 1 isoform 1						apoptosis|axon transport of mitochondrion|inner mitochondrial membrane organization|mitochondrial fission|mitochondrial fusion|positive regulation of anti-apoptosis|response to stimulus|visual perception	dendrite|integral to membrane|mitochondrial crista|mitochondrial intermembrane space|mitochondrial outer membrane	GTP binding|GTPase activity|magnesium ion binding|protein binding				0	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	194247692	194247699	+	IGR	DEL	GAAGGAAG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194247692_194247699delGAAGGAAG								ATP13A3 (58724 upstream) : TMEM44 (60704 downstream)																																			---	---	---	---
ACAP2	23527	broad.mit.edu	37	3	195095579	195095579	+	Intron	DEL	T	-	-	rs148359014		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195095579delT	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	195432772	195432772	+	Intron	DEL	G	-	-	rs113380974		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195432772delG	uc011btd.1	+						uc003fux.1_Intron					Homo sapiens cDNA FLJ46488 fis, clone THYMU3026869.																														---	---	---	---
KIAA0226	9711	broad.mit.edu	37	3	197401799	197401799	+	3'UTR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197401799delG	uc003fyc.2	-	20					KIAA0226_uc003fyd.3_3'UTR|MIR922_hsa-mir-922|MI0005714_5'Flank	NM_014687	NP_055502			hypothetical protein LOC9711 isoform 2.						autophagy|endocytosis|negative regulation of autophagy|negative regulation of endocytosis	early endosome|late endosome|lysosome	protein binding				0	all_cancers(143;8.26e-10)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.0446)														---	---	---	---
LRCH3	84859	broad.mit.edu	37	3	197560101	197560101	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197560101delT	uc011bul.1	+						LRCH3_uc003fyj.1_Intron|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)														---	---	---	---
ZNF721	170960	broad.mit.edu	37	4	484743	484743	+	Intron	DEL	A	-	-	rs75837326		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:484743delA	uc003gag.2	-						ZNF721_uc010ibe.2_Intron|ZNF721_uc003gah.1_Intron	NM_133474	NP_597731			zinc finger protein 721							intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1																		---	---	---	---
PIGG	54872	broad.mit.edu	37	4	520736	520736	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:520736delT	uc003gak.3	+						PIGG_uc003gaj.3_Intron|PIGG_uc011bux.1_Intron|PIGG_uc010ibf.2_Intron|PIGG_uc003gal.3_Intron	NM_001127178	NP_001120650			phosphatidylinositol glycan anchor biosynthesis,						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	CP2 mannose-ethanolamine phosphotransferase activity			central_nervous_system(2)|ovary(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	586727	586727	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:586727delA								PIGG (53408 upstream) : PDE6B (32636 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	1152420	1152420	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1152420delT								RNF212 (44838 upstream) : SPON2 (8302 downstream)																																			---	---	---	---
FAM53A	152877	broad.mit.edu	37	4	1675460	1675460	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1675460delA	uc011bve.1	-						FAM53A_uc010ibw.2_Intron	NM_001013622	NP_001013644			dorsal neural-tube nuclear protein							nucleus					0		all_epithelial(65;0.206)|Breast(71;0.212)	OV - Ovarian serous cystadenocarcinoma(23;0.0145)															---	---	---	---
WHSC1	7468	broad.mit.edu	37	4	1919853	1919853	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1919853delT	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_uc003geh.1_Intron	NM_001042424	NP_001035889			Wolf-Hirschhorn syndrome candidate 1 protein						anatomical structure morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|cytoplasm|nuclear membrane|nucleolus	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			ovary(3)|lung(3)|skin(2)|pancreas(1)	9		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)				T	IGH@	MM								---	---	---	---
WHSC1	7468	broad.mit.edu	37	4	1940129	1940129	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1940129delT	uc003gdz.3	+						WHSC1_uc003geb.3_Intron|WHSC1_uc003gec.3_Intron|WHSC1_uc003ged.3_Intron|WHSC1_uc003gee.3_Intron|WHSC1_uc003gef.3_Intron|WHSC1_uc003gei.3_5'Flank|WHSC1_uc003gdy.1_Intron|WHSC1_uc010icd.1_Intron|WHSC1_uc003gea.1_Intron|WHSC1_uc010ice.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	2214656	2214657	+	Intron	DEL	TT	-	-	rs75183121		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2214656_2214657delTT	uc003ger.2	-						POLN_uc011bvi.1_Intron	NM_181808	NP_861524			DNA-directed DNA polymerase nu						DNA repair|DNA replication	nucleus	DNA binding|DNA-directed DNA polymerase activity			kidney(2)|ovary(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(23;0.0955)										DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
POLN	353497	broad.mit.edu	37	4	2238431	2238431	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2238431delA	uc011bvi.1	-						HAUS3_uc011bvj.1_Intron|HAUS3_uc003ges.1_Intron|HAUS3_uc003get.1_Intron	NM_181808	NP_861524			DNA-directed DNA polymerase nu						DNA repair|DNA replication	nucleus	DNA binding|DNA-directed DNA polymerase activity			kidney(2)|ovary(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(23;0.0955)										DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
ZFYVE28	57732	broad.mit.edu	37	4	2285305	2285308	+	Intron	DEL	CCAT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2285305_2285308delCCAT	uc003gex.1	-						ZFYVE28_uc011bvk.1_Intron|ZFYVE28_uc011bvl.1_Intron|ZFYVE28_uc003gew.1_Intron	NM_020972	NP_066023			zinc finger, FYVE domain containing 28						negative regulation of epidermal growth factor receptor activity	cytosol|early endosome membrane	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			skin(2)|ovary(1)	3																		---	---	---	---
ZFYVE28	57732	broad.mit.edu	37	4	2352191	2352191	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2352191delA	uc003gex.1	-						ZFYVE28_uc011bvk.1_Intron|ZFYVE28_uc011bvl.1_Intron|ZFYVE28_uc003gey.3_Intron|ZFYVE28_uc003gez.2_Intron	NM_020972	NP_066023			zinc finger, FYVE domain containing 28						negative regulation of epidermal growth factor receptor activity	cytosol|early endosome membrane	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			skin(2)|ovary(1)	3																		---	---	---	---
RNF4	6047	broad.mit.edu	37	4	2508239	2508241	+	Intron	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2508239_2508241delTTT	uc003gfb.2	+						RNF4_uc010ici.1_Intron|RNF4_uc010icj.2_Intron|RNF4_uc003gfc.2_Intron	NM_002938	NP_002929			ring finger protein 4						androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|proteasomal ubiquitin-dependent protein catabolic process|protein autoubiquitination|protein K11-linked ubiquitination|protein K48-linked ubiquitination|protein K6-linked ubiquitination|protein K63-linked ubiquitination|regulation of kinetochore assembly|regulation of spindle assembly|response to arsenic-containing substance	cytoplasm|PML body	androgen receptor binding|DNA binding|nucleosome binding|sequence-specific DNA binding transcription factor activity|SUMO polymer binding|transcription coactivator activity|ubiquitin-protein ligase activity|zinc ion binding				0		all_epithelial(65;0.241)																---	---	---	---
FAM193A	8603	broad.mit.edu	37	4	2694778	2694779	+	Intron	DEL	TT	-	-	rs11342315		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2694778_2694779delTT	uc010icl.2	+						FAM193A_uc010ick.2_Intron|FAM193A_uc003gfd.2_Intron|FAM193A_uc011bvm.1_Intron|FAM193A_uc011bvn.1_Intron|FAM193A_uc011bvo.1_Intron|FAM193A_uc010icm.2_Intron|FAM193A_uc003gfe.2_Intron	NM_003704	NP_003695			hypothetical protein LOC8603											ovary(3)	3																		---	---	---	---
TNIP2	79155	broad.mit.edu	37	4	2747078	2747079	+	Intron	INS	-	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2747078_2747079insG	uc003gfg.2	-						TNIP2_uc003gff.2_Intron|TNIP2_uc003gfh.2_Intron	NM_024309	NP_077285			A20-binding inhibitor of NF-kappaB activation 2							cytosol	protein binding			central_nervous_system(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
ADD1	118	broad.mit.edu	37	4	2879695	2879695	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2879695delA	uc003gfr.2	+						ADD1_uc003gfn.2_Intron|ADD1_uc010ico.1_Intron|ADD1_uc003gfo.2_Intron|ADD1_uc003gfp.2_Intron|ADD1_uc003gfq.2_Intron|ADD1_uc003gfs.2_Intron|ADD1_uc003gft.3_Intron	NM_001119	NP_001110			adducin 1 (alpha) isoform a						actin filament bundle assembly|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|positive regulation of protein binding	cytosol|F-actin capping protein complex|nucleus|plasma membrane	actin filament binding|calmodulin binding|metal ion binding|protein heterodimerization activity|protein homodimerization activity|spectrin binding|transcription factor binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
GRK4	2868	broad.mit.edu	37	4	2977961	2977961	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2977961delT	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	2998285	2998285	+	Intron	DEL	A	-	-	rs79895601		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2998285delA	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	3100988	3100988	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3100988delT	uc011bvq.1	+							NM_002111	NP_002102			huntingtin						establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule	autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex	beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding			skin(2)|ovary(1)|lung(1)	4		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)														---	---	---	---
RGS12	6002	broad.mit.edu	37	4	3313166	3313167	+	5'Flank	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3313166_3313167insT	uc003ggw.2	+						RGS12_uc003ggu.2_Intron|RGS12_uc010ics.1_Intron|RGS12_uc011bvr.1_Intron|RGS12_uc003ggv.2_5'Flank	NM_198229	NP_937872			regulator of G-protein signalling 12 isoform 1							condensed nuclear chromosome|cytoplasm|plasma membrane	GTPase activator activity|receptor signaling protein activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
RGS12	6002	broad.mit.edu	37	4	3400465	3400465	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3400465delA	uc003ggw.2	+						RGS12_uc003ggu.2_Intron|RGS12_uc010ics.1_Intron|RGS12_uc011bvr.1_Intron|RGS12_uc003ggv.2_Intron|RGS12_uc003ggy.1_Intron|RGS12_uc010ict.1_Intron|RGS12_uc003ggz.2_Intron|RGS12_uc010icu.1_Intron|RGS12_uc011bvs.1_Intron|RGS12_uc003gha.2_Intron|RGS12_uc010icv.2_Intron	NM_198229	NP_937872			regulator of G-protein signalling 12 isoform 1							condensed nuclear chromosome|cytoplasm|plasma membrane	GTPase activator activity|receptor signaling protein activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	3749065	3749065	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3749065delA								LRPAP1 (214841 upstream) : ADRA2C (19010 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	3961006	3961006	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3961006delA								LOC348926 (3858 upstream) : OTOP1 (229524 downstream)																																			---	---	---	---
ZBTB49	166793	broad.mit.edu	37	4	4300157	4300157	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4300157delT	uc003ghu.2	+						ZBTB49_uc003ghv.2_Intron|ZBTB49_uc010icy.2_Intron	NM_145291	NP_660334			zinc finger protein 509						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	4599356	4599356	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4599356delA	uc003gid.2	+											Homo sapiens, clone IMAGE:5204729, mRNA.																														---	---	---	---
EVC2	132884	broad.mit.edu	37	4	5612519	5612521	+	Intron	DEL	TTC	-	-	rs10690279		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5612519_5612521delTTC	uc003gij.2	-						EVC2_uc011bwb.1_Intron|EVC2_uc003gik.2_Intron	NM_147127	NP_667338			limbin							integral to membrane				large_intestine(3)|ovary(2)	5																		---	---	---	---
EVC2	132884	broad.mit.edu	37	4	5640123	5640125	+	Intron	DEL	AAA	-	-	rs34116303		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5640123_5640125delAAA	uc003gij.2	-						EVC2_uc011bwb.1_Intron|EVC2_uc003gik.2_Intron	NM_147127	NP_667338			limbin							integral to membrane				large_intestine(3)|ovary(2)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	6307072	6307072	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6307072delT								WFS1 (2081 upstream) : PPP2R2C (15234 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	6733864	6733864	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6733864delT								CNO (14477 upstream) : KIAA0232 (50595 downstream)																																			---	---	---	---
KIAA0232	9778	broad.mit.edu	37	4	6882470	6882470	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6882470delA	uc003gjr.3	+						KIAA0232_uc003gjq.3_Intron	NM_014743	NP_055558			hypothetical protein LOC9778								ATP binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	7133096	7133097	+	IGR	INS	-	ATAA	ATAA			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7133096_7133097insATAA								FLJ36777 (27993 upstream) : SORCS2 (61277 downstream)																																			---	---	---	---
SORCS2	57537	broad.mit.edu	37	4	7620565	7620566	+	Intron	DEL	AC	-	-	rs71872025		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7620565_7620566delAC	uc003gkb.3	+						SORCS2_uc011bwi.1_Intron	NM_020777	NP_065828			VPS10 domain receptor protein SORCS 2 precursor							integral to membrane	neuropeptide receptor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
ABLIM2	84448	broad.mit.edu	37	4	8091850	8091850	+	Intron	DEL	T	-	-	rs13136604	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8091850delT	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																		---	---	---	---
SH3TC1	54436	broad.mit.edu	37	4	8219843	8219844	+	Intron	DEL	AT	-	-	rs1281137	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8219843_8219844delAT	uc003gkv.3	+						SH3TC1_uc003gkw.3_Intron|SH3TC1_uc003gkx.3_Intron	NM_018986	NP_061859			SH3 domain and tetratricopeptide repeats 1								binding			large_intestine(2)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	10241132	10241132	+	IGR	DEL	C	-	-	rs917821	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10241132delC								WDR1 (122559 upstream) : ZNF518B (200373 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	11316851	11316851	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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	11450294	11450294	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11450294delT								HS3ST1 (19757 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	11456336	11456336	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11456336delA								HS3ST1 (25799 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	11844014	11844015	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11844014_11844015delTT								HS3ST1 (413477 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	12579255	12579255	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12579255delA								None (None upstream) : HSP90AB2P (755782 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	13112786	13112786	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13112786delA								None (None upstream) : HSP90AB2P (222251 downstream)																																			---	---	---	---
RAB28	9364	broad.mit.edu	37	4	13370445	13370445	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13370445delT	uc003gmu.2	-						RAB28_uc003gmt.2_Intron|RAB28_uc011bwz.1_Intron|RAB28_uc003gmv.2_Intron	NM_001017979	NP_001017979			RAB28, member RAS oncogene family isoform 1						small GTPase mediated signal transduction	plasma membrane	GDP binding|GTP binding|GTPase activity			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	13674136	13674136	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13674136delA	uc003gna.1	+											Homo sapiens cDNA FLJ34570 fis, clone KIDNE2008072.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	13753547	13753554	+	Intron	DEL	CCATCCAT	-	-	rs3973902		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13753547_13753554delCCATCCAT	uc003gna.1	+											Homo sapiens cDNA FLJ34570 fis, clone KIDNE2008072.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	13764890	13764891	+	Intron	DEL	TT	-	-	rs141911363		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13764890_13764891delTT	uc003gna.1	+											Homo sapiens cDNA FLJ34570 fis, clone KIDNE2008072.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	14490601	14490601	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:14490601delA	uc003gne.2	-						uc003gnf.2_Intron					Homo sapiens cDNA clone IMAGE:3604199, **** WARNING: chimeric clone ****.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	14506382	14506382	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:14506382delT	uc003gne.2	-						uc003gnf.2_Intron					Homo sapiens cDNA clone IMAGE:3604199, **** WARNING: chimeric clone ****.																														---	---	---	---
CPEB2	132864	broad.mit.edu	37	4	15059946	15059946	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15059946delT	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	15697700	15697701	+	IGR	DEL	TT	-	-	rs33977519		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15697700_15697701delTT								FAM200B (5638 upstream) : BST1 (6872 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	16416567	16416567	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16416567delA								FLJ39653 (156757 upstream) : LDB2 (86600 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	16966544	16966544	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16966544delT								LDB2 (66120 upstream) : QDPR (521476 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	18518743	18518743	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:18518743delA								LCORL (495358 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	19236239	19236239	+	IGR	DEL	T	-	-	rs33958578		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:19236239delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	19250817	19250817	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:19250817delT								None (None upstream) : None (None downstream)																																			---	---	---	---
KCNIP4	80333	broad.mit.edu	37	4	21070851	21070851	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21070851delT	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	21192130	21192130	+	Intron	DEL	G	-	-	rs66685938		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21192130delG	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	22235995	22235996	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22235995_22235996delTT								KCNIP4 (285621 upstream) : GPR125 (153003 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	22849026	22849027	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22849026_22849027delAA								GBA3 (27835 upstream) : PPARGC1A (944618 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	23244687	23244689	+	IGR	DEL	TTT	-	-	rs150206135		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23244687_23244689delTTT								GBA3 (423496 upstream) : PPARGC1A (548956 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	23333191	23333191	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23333191delA								GBA3 (512000 upstream) : PPARGC1A (460454 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	24117061	24117061	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24117061delA								PPARGC1A (225361 upstream) : MIR573 (404754 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	25306865	25306865	+	IGR	DEL	A	-	-	rs36030414		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25306865delA								PI4K2B (26034 upstream) : ZCCHC4 (7531 downstream)																																			---	---	---	---
ZCCHC4	29063	broad.mit.edu	37	4	25370275	25370275	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25370275delA	uc003grl.3	+						ZCCHC4_uc003grn.3_Intron	NM_024936	NP_079212			zinc finger, CCHC domain containing 4								methyltransferase activity|nucleic acid binding|zinc ion binding			ovary(2)	2		Breast(46;0.0503)																---	---	---	---
ANAPC4	29945	broad.mit.edu	37	4	25416208	25416208	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25416208delT	uc003gro.2	+						ANAPC4_uc003grp.2_Intron|ANAPC4_uc003grq.2_Intron	NM_013367	NP_037499			anaphase-promoting complex subunit 4						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G2/M transition of mitotic cell cycle|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm	protein phosphatase binding|ubiquitin-protein ligase activity			ovary(2)|large_intestine(1)|pancreas(1)|skin(1)	5		Breast(46;0.0503)																---	---	---	---
SLC34A2	10568	broad.mit.edu	37	4	25664605	25664605	+	Intron	DEL	T	-	-	rs34583336		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25664605delT	uc003grr.2	+						SLC34A2_uc003grs.2_Intron|SLC34A2_uc010iev.2_Intron	NM_006424	NP_006415			solute carrier family 34 (sodium phosphate),						cellular phosphate ion homeostasis	apical plasma membrane|brush border membrane|integral to plasma membrane	phosphate binding|sodium ion binding|sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity			skin(3)|ovary(1)|kidney(1)	5		Breast(46;0.0503)																---	---	---	---
SEL1L3	23231	broad.mit.edu	37	4	25842153	25842154	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25842153_25842154insA	uc003gru.3	-							NM_015187	NP_056002			sel-1 suppressor of lin-12-like 3							integral to membrane	binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	25935666	25935666	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25935666delA								C4orf52 (4166 upstream) : RBPJ (385666 downstream)																																			---	---	---	---
TBC1D19	55296	broad.mit.edu	37	4	26587214	26587214	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26587214delT	uc003gsf.3	+						TBC1D19_uc010iew.2_Intron|TBC1D19_uc011bxu.1_Intron	NM_018317	NP_060787			TBC1 domain family, member 19							intracellular	Rab GTPase activator activity			breast(1)	1		Breast(46;0.0503)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	26780037	26780038	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26780037_26780038insA								TBC1D19 (23122 upstream) : STIM2 (82326 downstream)																																			---	---	---	---
STIM2	57620	broad.mit.edu	37	4	26860027	26860031	+	5'Flank	DEL	AAGGA	-	-	rs147233613		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26860027_26860031delAAGGA	uc003gsh.3	+						STIM2_uc003gsg.3_5'Flank|STIM2_uc010iex.2_5'Flank	NM_020860	NP_065911			stromal interaction molecule 2						activation of store-operated calcium channel activity|calcium ion transport|cellular calcium ion homeostasis|negative regulation of calcium ion transport via store-operated calcium channel activity	endoplasmic reticulum membrane|integral to membrane|plasma membrane	calcium channel regulator activity|calcium ion binding|protein binding			central_nervous_system(1)|skin(1)	2		Breast(46;0.0503)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	28193704	28193705	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:28193704_28193705delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	28546540	28546540	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:28546540delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	29802889	29802889	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:29802889delT								None (None upstream) : PCDH7 (919148 downstream)																																			---	---	---	---
PCDH7	5099	broad.mit.edu	37	4	30896867	30896867	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30896867delA	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	31575519	31575519	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:31575519delA								PCDH7 (427098 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	32087399	32087399	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:32087399delA								PCDH7 (938978 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	32371668	32371669	+	IGR	DEL	AC	-	-	rs35643814		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:32371668_32371669delAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	32988982	32988982	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:32988982delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	33228103	33228103	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:33228103delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	34015239	34015239	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:34015239delT	uc003gsn.2	-											Homo sapiens, clone IMAGE:5172449, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	35542927	35542927	+	IGR	DEL	T	-	-	rs112498957		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:35542927delT								None (None upstream) : ARAP2 (406917 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	35763902	35763902	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:35763902delA								None (None upstream) : ARAP2 (185942 downstream)																																			---	---	---	---
ARAP2	116984	broad.mit.edu	37	4	36047804	36047805	+	Intron	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36047804_36047805delTC	uc003gso.2	-											Homo sapiens cDNA clone IMAGE:5296543.						regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytosol	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
ARAP2	116984	broad.mit.edu	37	4	36158170	36158170	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36158170delT	uc003gsq.1	-							NM_015230	NP_056045			ArfGAP with RhoGAP domain, ankyrin repeat and PH						regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytosol	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
DTHD1	401124	broad.mit.edu	37	4	36342526	36342526	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36342526delA	uc011bxy.1	+						DTHD1_uc003gsv.2_Intron	NM_001136536	NP_001130008			death domain containing 1						signal transduction						0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	37113888	37113890	+	IGR	DEL	TTT	-	-	rs79139913		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37113888_37113890delTTT								MIR1255B-1 (685838 upstream) : KIAA1239 (132800 downstream)																																			---	---	---	---
KIAA1239	57495	broad.mit.edu	37	4	37322178	37322178	+	Intron	DEL	G	-	-	rs5857560		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37322178delG	uc011bxz.1	+							NM_001144990	NP_001138462			hypothetical protein LOC57495												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	37886454	37886461	+	IGR	DEL	GTGTGTGT	-	-	rs58761577	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37886454_37886461delGTGTGTGT								PGM2 (21895 upstream) : TBC1D1 (6259 downstream)																																			---	---	---	---
TBC1D1	23216	broad.mit.edu	37	4	38054381	38054386	+	Intron	DEL	ACACAG	-	-	rs60149486		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38054381_38054386delACACAG	uc003gtb.2	+						TBC1D1_uc011byd.1_Intron|TBC1D1_uc010ifd.2_Intron|TBC1D1_uc011byf.1_Intron	NM_015173	NP_055988			TBC1 (tre-2/USP6, BUB2, cdc16) domain family,							nucleus	Rab GTPase activator activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	38328657	38328658	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38328657_38328658insT								TBC1D1 (187864 upstream) : FLJ13197 (285664 downstream)																																			---	---	---	---
FLJ13197	79667	broad.mit.edu	37	4	38624425	38624428	+	Intron	DEL	AGAT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38624425_38624428delAGAT	uc003gte.1	-							NR_026804				Homo sapiens clone pp6414 unknown mRNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	38743731	38743731	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38743731delA								KLF3 (40603 upstream) : TLR10 (30532 downstream)																																			---	---	---	---
FAM114A1	92689	broad.mit.edu	37	4	38907022	38907022	+	Intron	DEL	A	-	-	rs73236670	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38907022delA	uc003gtn.2	+						FAM114A1_uc011byh.1_Intron	NM_138389	NP_612398			hypothetical protein LOC92689							cytoplasm				ovary(1)	1																		---	---	---	---
LIAS	11019	broad.mit.edu	37	4	39478849	39478850	+	3'UTR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39478849_39478850delAA	uc003guf.2	+	11					LIAS_uc003gug.2_3'UTR|LIAS_uc003guh.2_3'UTR	NM_006859	NP_006850			lipoic acid synthetase isoform 1 precursor						inflammatory response|response to lipopolysaccharide|response to oxidative stress	mitochondrion	4 iron, 4 sulfur cluster binding|lipoate synthase activity|metal ion binding				0					Lipoic Acid(DB00166)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	39657858	39657860	+	IGR	DEL	TTT	-	-	rs34185140		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39657858_39657860delTTT								C4orf34 (17377 upstream) : UBE2K (41804 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	39686945	39686945	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39686945delA								C4orf34 (46464 upstream) : UBE2K (12719 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	40167283	40167284	+	IGR	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40167283_40167284delGT								N4BP2 (10266 upstream) : RHOH (31243 downstream)																																			---	---	---	---
LIMCH1	22998	broad.mit.edu	37	4	41594726	41594726	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41594726delC	uc003gvu.3	+						LIMCH1_uc003gvt.1_Intron|LIMCH1_uc003gvv.3_Intron|LIMCH1_uc003gvw.3_Intron|LIMCH1_uc003gvx.3_Intron|LIMCH1_uc003gwe.3_Intron|LIMCH1_uc003gvy.3_Intron|LIMCH1_uc003gwa.3_Intron|LIMCH1_uc003gvz.3_Intron	NM_014988	NP_055803			LIM and calponin homology domains 1 isoform a						actomyosin structure organization		actin binding|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	42224664	42224664	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42224664delG								BEND4 (69769 upstream) : SHISA3 (175192 downstream)																																			---	---	---	---
ATP8A1	10396	broad.mit.edu	37	4	42576524	42576524	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42576524delA	uc003gwr.2	-						ATP8A1_uc003gws.2_Intron|ATP8A1_uc011byz.1_Intron	NM_006095	NP_006086			ATPase, aminophospholipid transporter (APLT),						ATP biosynthetic process	chromaffin granule membrane|integral to membrane|plasma membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			skin(2)|central_nervous_system(1)	3					Phosphatidylserine(DB00144)													---	---	---	---
ATP8A1	10396	broad.mit.edu	37	4	42644007	42644007	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42644007delT	uc003gwr.2	-						ATP8A1_uc003gws.2_Intron|ATP8A1_uc011byz.1_Intron	NM_006095	NP_006086			ATPase, aminophospholipid transporter (APLT),						ATP biosynthetic process	chromaffin granule membrane|integral to membrane|plasma membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			skin(2)|central_nervous_system(1)	3					Phosphatidylserine(DB00144)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	42757630	42757630	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42757630delT								ATP8A1 (98508 upstream) : GRXCR1 (137654 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	42824225	42824225	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42824225delA								ATP8A1 (165103 upstream) : GRXCR1 (71059 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	42839675	42839676	+	IGR	INS	-	TC	TC	rs143302076	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42839675_42839676insTC								ATP8A1 (180553 upstream) : GRXCR1 (55608 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	42865392	42865392	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42865392delT								ATP8A1 (206270 upstream) : GRXCR1 (29892 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	43523764	43523765	+	IGR	INS	-	T	T	rs144359672	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:43523764_43523765insT								GRXCR1 (491091 upstream) : KCTD8 (652157 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	43550269	43550269	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:43550269delT								GRXCR1 (517596 upstream) : KCTD8 (625653 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	43901421	43901421	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:43901421delA								GRXCR1 (868748 upstream) : KCTD8 (274501 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	45144990	45145001	+	IGR	DEL	TTCATTCCTTCT	-	-	rs71192218		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:45144990_45145001delTTCATTCCTTCT								GNPDA2 (416378 upstream) : GABRG1 (892788 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	46004555	46004555	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46004555delC								None (None upstream) : GABRG1 (33234 downstream)																																			---	---	---	---
COX7B2	170712	broad.mit.edu	37	4	46898663	46898663	+	Intron	DEL	A	-	-	rs66480334		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46898663delA	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	47018509	47018509	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47018509delT								GABRA4 (22929 upstream) : GABRB1 (14786 downstream)																																			---	---	---	---
NFXL1	152518	broad.mit.edu	37	4	47853778	47853779	+	Intron	DEL	AT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47853778_47853779delAT	uc010igh.2	-						NFXL1_uc003gxo.2_Intron|NFXL1_uc003gxp.2_Intron|NFXL1_uc003gxq.3_Intron|NFXL1_uc010igi.2_Intron	NM_152995	NP_694540			nuclear transcription factor, X-box binding-like							integral to membrane|nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
NFXL1	152518	broad.mit.edu	37	4	47862876	47862876	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47862876delT	uc010igh.2	-						NFXL1_uc003gxo.2_Intron|NFXL1_uc003gxp.2_Intron|NFXL1_uc003gxq.3_Intron|NFXL1_uc010igi.2_Intron	NM_152995	NP_694540			nuclear transcription factor, X-box binding-like							integral to membrane|nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
NFXL1	152518	broad.mit.edu	37	4	47899965	47899965	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47899965delA	uc010igh.2	-						NFXL1_uc003gxp.2_Intron|NFXL1_uc003gxq.3_Intron|NFXL1_uc010igi.2_Intron	NM_152995	NP_694540			nuclear transcription factor, X-box binding-like							integral to membrane|nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
NIPAL1	152519	broad.mit.edu	37	4	48038331	48038331	+	3'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48038331delT	uc003gxw.2	+	6						NM_207330	NP_997213			NIPA-like domain containing 1							integral to membrane					0																		---	---	---	---
TEC	7006	broad.mit.edu	37	4	48242974	48242975	+	Intron	DEL	AA	-	-	rs75046804		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48242974_48242975delAA	uc003gxz.2	-							NM_003215	NP_003206			tec protein tyrosine kinase						intracellular protein kinase cascade	cytosol	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(4)|stomach(1)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)	9																		---	---	---	---
SLAIN2	57606	broad.mit.edu	37	4	48420186	48420187	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48420186_48420187delTT	uc003gya.3	+							NM_020846	NP_065897			SLAIN motif family, member 2							centrosome					0																		---	---	---	---
FRYL	285527	broad.mit.edu	37	4	48625212	48625213	+	Intron	DEL	AC	-	-	rs776579	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48625212_48625213delAC	uc003gyh.1	-						FRYL_uc003gyk.2_Intron|FRYL_uc003gyl.1_Intron|FRYL_uc003gym.1_Intron	NM_015030	NP_055845			furry-like						regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	49109121	49109135	+	IGR	DEL	CATGCCAGTTGATTG	-	-	rs146579353	by1000genomes;by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49109121_49109135delCATGCCAGTTGATTG								CWH43 (45028 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49220041	49220041	+	IGR	DEL	A	-	-	rs35986529		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49220041delA								CWH43 (155948 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49554994	49554994	+	IGR	DEL	C	-	-	rs10440609		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49554994delC								CWH43 (490901 upstream) : None (None downstream)																																			---	---	---	---
SGCB	6443	broad.mit.edu	37	4	52903717	52903718	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:52903717_52903718delAC	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	53234114	53234115	+	IGR	DEL	GG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53234114_53234115delGG								SPATA18 (270657 upstream) : USP46 (223014 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	53285046	53285047	+	IGR	DEL	AC	-	-	rs34400314		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53285046_53285047delAC								SPATA18 (321589 upstream) : USP46 (172082 downstream)																																			---	---	---	---
SCFD2	152579	broad.mit.edu	37	4	53893425	53893425	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53893425delT	uc003gzu.2	-						SCFD2_uc010igm.2_Intron	NM_152540	NP_689753			sec1 family domain containing 2						protein transport|vesicle docking involved in exocytosis					ovary(2)|pancreas(1)	3			GBM - Glioblastoma multiforme(3;1.07e-26)|LUSC - Lung squamous cell carcinoma(32;0.0134)															---	---	---	---
SCFD2	152579	broad.mit.edu	37	4	53988101	53988101	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53988101delT	uc003gzu.2	-						SCFD2_uc010igm.2_Intron	NM_152540	NP_689753			sec1 family domain containing 2						protein transport|vesicle docking involved in exocytosis					ovary(2)|pancreas(1)	3			GBM - Glioblastoma multiforme(3;1.07e-26)|LUSC - Lung squamous cell carcinoma(32;0.0134)															---	---	---	---
KDR	3791	broad.mit.edu	37	4	55967070	55967071	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55967070_55967071delAA	uc003has.2	-						KDR_uc003hat.1_Intron	NM_002253	NP_002244			kinase insert domain receptor precursor						angiogenesis|cell differentiation|interspecies interaction between organisms|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of focal adhesion assembly|positive regulation of positive chemotaxis|regulation of cell shape	integral to plasma membrane	ATP binding|growth factor binding|Hsp90 protein binding|integrin binding|receptor signaling protein tyrosine kinase activity|vascular endothelial growth factor receptor activity			lung(16)|soft_tissue(4)|central_nervous_system(4)|large_intestine(2)|stomach(2)|skin(2)|ovary(2)|kidney(1)	33	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Sorafenib(DB00398)|Sunitinib(DB01268)			Mis		NSCLC|angiosarcoma				Familial_Infantile_Hemangioma	TSP Lung(20;0.16)			---	---	---	---
KDR	3791	broad.mit.edu	37	4	55972313	55972313	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55972313delT	uc003has.2	-						KDR_uc003hat.1_Intron|KDR_uc011bzx.1_Intron	NM_002253	NP_002244			kinase insert domain receptor precursor						angiogenesis|cell differentiation|interspecies interaction between organisms|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of focal adhesion assembly|positive regulation of positive chemotaxis|regulation of cell shape	integral to plasma membrane	ATP binding|growth factor binding|Hsp90 protein binding|integrin binding|receptor signaling protein tyrosine kinase activity|vascular endothelial growth factor receptor activity			lung(16)|soft_tissue(4)|central_nervous_system(4)|large_intestine(2)|stomach(2)|skin(2)|ovary(2)|kidney(1)	33	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Sorafenib(DB00398)|Sunitinib(DB01268)			Mis		NSCLC|angiosarcoma				Familial_Infantile_Hemangioma	TSP Lung(20;0.16)			---	---	---	---
SRD5A3	79644	broad.mit.edu	37	4	56217825	56217826	+	Intron	DEL	AA	-	-	rs34820507		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56217825_56217826delAA	uc003hau.2	+							NM_024592	NP_078868			steroid 5 alpha-reductase 3						androgen biosynthetic process|dolichol metabolic process|dolichol-linked oligosaccharide biosynthetic process|polyprenol catabolic process	endoplasmic reticulum membrane|integral to membrane	3-oxo-5-alpha-steroid 4-dehydrogenase activity|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor				0	all_cancers(7;0.0308)|all_lung(4;0.00195)|Lung NSC(11;0.00431)|all_epithelial(27;0.0425)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.0179)															---	---	---	---
NMU	10874	broad.mit.edu	37	4	56463557	56463557	+	Intron	DEL	T	-	-	rs35319564		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56463557delT	uc003hbc.2	-							NM_006681	NP_006672			neuromedin U precursor						neuropeptide signaling pathway	extracellular region					0	Lung NSC(11;0.00256)|all_epithelial(27;0.075)|Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.103)	LUSC - Lung squamous cell carcinoma(4;6.72e-08)|Lung(4;6.22e-07)|Epithelial(7;0.00559)	LUSC - Lung squamous cell carcinoma(721;0.0115)														---	---	---	---
CEP135	9662	broad.mit.edu	37	4	56838317	56838317	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56838317delA	uc003hbi.2	+						CEP135_uc003hbj.2_Intron	NM_025009	NP_079285			centrosome protein 4						centriole replication|centriole-centriole cohesion|G2/M transition of mitotic cell cycle	centriole|cytosol	protein C-terminus binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5	Glioma(25;0.08)|all_neural(26;0.101)																	---	---	---	---
CEP135	9662	broad.mit.edu	37	4	56872644	56872646	+	Intron	DEL	GTG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56872644_56872646delGTG	uc003hbi.2	+						CEP135_uc003hbj.2_Intron	NM_025009	NP_079285			centrosome protein 4						centriole replication|centriole-centriole cohesion|G2/M transition of mitotic cell cycle	centriole|cytosol	protein C-terminus binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5	Glioma(25;0.08)|all_neural(26;0.101)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	57736637	57736637	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57736637delA								SPINK2 (48744 upstream) : REST (37405 downstream)																																			---	---	---	---
REST	5978	broad.mit.edu	37	4	57783195	57783198	+	Intron	DEL	TCTG	-	-	rs147452343		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57783195_57783198delTCTG	uc003hch.2	+						REST_uc003hci.2_Intron|REST_uc010ihf.2_Intron	NM_005612	NP_005603			RE1-silencing transcription factor						cardiac muscle cell myoblast differentiation|cellular response to drug|cellular response to electrical stimulus|cellular response to glucocorticoid stimulus|histone H4 deacetylation|negative regulation by host of viral transcription|negative regulation of aldosterone biosynthetic process|negative regulation of calcium ion-dependent exocytosis|negative regulation of cell proliferation|negative regulation of cortisol biosynthetic process|negative regulation of dense core granule biogenesis|negative regulation of insulin secretion|negative regulation of mesenchymal stem cell differentiation|negative regulation of neurogenesis|negative regulation of neuron differentiation|positive regulation of apoptosis|positive regulation of caspase activity|positive regulation of transcription, DNA-dependent	cytoplasm|transcriptional repressor complex	calcium channel activity|chromatin binding|core promoter proximal region sequence-specific DNA binding|core promoter sequence-specific DNA binding|outward rectifier potassium channel activity|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|zinc ion binding			skin(5)|upper_aerodigestive_tract(1)|ovary(1)|lung(1)|central_nervous_system(1)	9	Glioma(25;0.08)|all_neural(26;0.181)																	---	---	---	---
POLR2B	5431	broad.mit.edu	37	4	57889309	57889309	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57889309delT	uc003hcl.1	+						POLR2B_uc011cae.1_Intron|POLR2B_uc011caf.1_Intron|POLR2B_uc003hcm.1_Intron	NM_000938	NP_000929			DNA directed RNA polymerase II polypeptide B						mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|protein binding|ribonucleoside binding			ovary(2)	2	Glioma(25;0.08)|all_neural(26;0.181)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	58168663	58168663	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58168663delT								IGFBP7 (192124 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	58487881	58487882	+	IGR	INS	-	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58487881_58487882insC								IGFBP7 (511342 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	60012350	60012350	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:60012350delT								None (None upstream) : None (None downstream)																																			---	---	---	---
LPHN3	23284	broad.mit.edu	37	4	62738374	62738374	+	Intron	DEL	A	-	-	rs112560667		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62738374delA	uc010ihh.2	+						LPHN3_uc003hcq.3_Intron|LPHN3_uc003hcs.1_Intron	NM_015236	NP_056051			latrophilin 3 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18																		---	---	---	---
LPHN3	23284	broad.mit.edu	37	4	62862965	62862968	+	Intron	DEL	AAAA	-	-	rs78439836		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62862965_62862968delAAAA	uc010ihh.2	+						LPHN3_uc003hcq.3_Intron|LPHN3_uc003hct.2_Intron	NM_015236	NP_056051			latrophilin 3 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	63072685	63072687	+	IGR	DEL	TTC	-	-	rs58353498		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63072685_63072687delTTC								LPHN3 (134518 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	63376652	63376652	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63376652delT								LPHN3 (438485 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	64217248	64217248	+	IGR	DEL	A	-	-	rs35934382		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:64217248delA								None (None upstream) : TECRL (926937 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	64475079	64475079	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:64475079delA								None (None upstream) : TECRL (669106 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	64580107	64580107	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:64580107delA								None (None upstream) : TECRL (564078 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	64878522	64878523	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:64878522_64878523delAA								None (None upstream) : TECRL (265662 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	65699433	65699433	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:65699433delA								TECRL (424255 upstream) : EPHA5 (485849 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	65731418	65731418	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:65731418delA								TECRL (456240 upstream) : EPHA5 (453864 downstream)																																			---	---	---	---
EPHA5	2044	broad.mit.edu	37	4	66256048	66256048	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66256048delT	uc003hcy.2	-						EPHA5_uc003hcx.2_Intron|EPHA5_uc003hcz.2_Intron|EPHA5_uc011cah.1_Intron|EPHA5_uc011cai.1_Intron|EPHA5_uc003hda.2_Intron	NM_004439	NP_004430			ephrin receptor EphA5 isoform a precursor						cAMP-mediated signaling|neuron development	dendrite|external side of plasma membrane|integral to plasma membrane|neuronal cell body|perinuclear region of cytoplasm|rough endoplasmic reticulum	ATP binding|transmembrane-ephrin receptor activity			lung(19)|stomach(2)|ovary(2)|central_nervous_system(1)	24															TSP Lung(17;0.13)			---	---	---	---
EPHA5	2044	broad.mit.edu	37	4	66361006	66361006	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66361006delT	uc003hcy.2	-						EPHA5_uc003hcx.2_Intron|EPHA5_uc003hcz.2_Intron|EPHA5_uc011cah.1_Intron|EPHA5_uc011cai.1_Intron|EPHA5_uc003hda.2_Intron	NM_004439	NP_004430			ephrin receptor EphA5 isoform a precursor						cAMP-mediated signaling|neuron development	dendrite|external side of plasma membrane|integral to plasma membrane|neuronal cell body|perinuclear region of cytoplasm|rough endoplasmic reticulum	ATP binding|transmembrane-ephrin receptor activity			lung(19)|stomach(2)|ovary(2)|central_nervous_system(1)	24															TSP Lung(17;0.13)			---	---	---	---
Unknown	0	broad.mit.edu	37	4	67222131	67222131	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67222131delT								MIR1269 (79485 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	67536850	67536851	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67536850_67536851delAA								MIR1269 (394204 upstream) : CENPC1 (801138 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	67755298	67755298	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67755298delA								MIR1269 (612652 upstream) : CENPC1 (582691 downstream)																																			---	---	---	---
UBA6	55236	broad.mit.edu	37	4	68529846	68529846	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68529846delA	uc003hdg.3	-						UBA6_uc003hdi.2_Intron|UBA6_uc003hdj.2_Intron	NM_018227	NP_060697			ubiquitin-activating enzyme E1-like 2						protein ubiquitination|ubiquitin-dependent protein catabolic process	cytoplasm	ATP binding|FAT10 activating enzyme activity|ligase activity|protein binding				0																		---	---	---	---
LOC550112	550112	broad.mit.edu	37	4	68685139	68685139	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68685139delA	uc003hdl.3	+											Homo sapiens chromosome 4 cDNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	69263568	69263569	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69263568_69263569insT								YTHDC1 (47744 upstream) : UGT2B15 (248747 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	69279404	69279404	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69279404delT								YTHDC1 (63580 upstream) : UGT2B15 (232912 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	70267902	70267902	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70267902delA								UGT2B28 (107135 upstream) : UGT2B4 (77982 downstream)																																			---	---	---	---
UGT2A1	10941	broad.mit.edu	37	4	70466528	70466528	+	Intron	DEL	A	-	-	rs72053280		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70466528delA	uc003hem.3	-						UGT2A1_uc011caq.1_Intron|UGT2A1_uc010ihu.2_Intron|UGT2A1_uc010iht.2_Intron|UGT2A1_uc010ihs.2_Intron	NM_006798	NP_006789			UDP glucuronosyltransferase 2 family,						detection of chemical stimulus|sensory perception of smell	integral to membrane	glucuronosyltransferase activity|glucuronosyltransferase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	70955081	70955082	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70955081_70955082insA								CSN1S2A (4095 upstream) : C4orf40 (62711 downstream)																																			---	---	---	---
C4orf40	401137	broad.mit.edu	37	4	71021623	71021623	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71021623delA	uc003hfa.3	+						C4orf40_uc003hfb.3_Intron	NM_214711	NP_999876			hypothetical protein LOC401137 precursor							extracellular region					0																		---	---	---	---
MOBKL1A	92597	broad.mit.edu	37	4	71812541	71812541	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71812541delA	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)															---	---	---	---
MOBKL1A	92597	broad.mit.edu	37	4	71817592	71817592	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71817592delA	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	73039151	73039151	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73039151delC								NPFFR2 (20403 upstream) : ADAMTS3 (107536 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	73840224	73840227	+	IGR	DEL	TCTG	-	-	rs72483634		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73840224_73840227delTCTG								ADAMTS3 (405708 upstream) : COX18 (80189 downstream)																																			---	---	---	---
ANKRD17	26057	broad.mit.edu	37	4	74007867	74007867	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74007867delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	74434572	74434573	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74434572_74434573delTT								AFM (64855 upstream) : RASSF6 (4289 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	76228901	76228901	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76228901delA								PARM1 (253578 upstream) : RCHY1 (175454 downstream)																																			---	---	---	---
G3BP2	9908	broad.mit.edu	37	4	76568664	76568664	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76568664delA	uc003hir.2	-	12					G3BP2_uc003his.2_3'UTR|G3BP2_uc003hit.2_3'UTR	NM_012297	NP_036429			Ras-GTPase activating protein SH3 domain-binding						cytoplasmic sequestering of NF-kappaB|mRNA transport|Ras protein signal transduction|regulation of small GTPase mediated signal transduction	cytosol	GTPase activator activity|nucleotide binding|receptor signaling complex scaffold activity|RNA binding			breast(2)|central_nervous_system(1)	3			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)															---	---	---	---
USO1	8615	broad.mit.edu	37	4	76649959	76649959	+	5'UTR	DEL	T	-	-	rs147239968		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76649959delT	uc003hiu.2	+	1					uc010iiy.2_5'Flank	NM_003715	NP_003706			USO1 homolog, vesicle docking protein						intracellular protein transport|vesicle fusion with Golgi apparatus	cytosol|Golgi membrane	protein binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)															---	---	---	---
NUP54	53371	broad.mit.edu	37	4	77047019	77047020	+	Intron	DEL	GA	-	-	rs71844760		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77047019_77047020delGA	uc003hjs.2	-						NUP54_uc010ije.2_Intron|NUP54_uc011cbs.1_Intron|NUP54_uc011cbt.1_Intron|NUP54_uc003hjt.2_Intron	NM_017426	NP_059122			nucleoporin 54kDa						carbohydrate metabolic process|glucose transport|mRNA transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytoplasm|nuclear membrane|nuclear pore|nucleoplasm				ovary(1)|lung(1)	2																		---	---	---	---
NUP54	53371	broad.mit.edu	37	4	77064232	77064232	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77064232delA	uc003hjs.2	-						NUP54_uc010ije.2_Intron|NUP54_uc011cbs.1_Intron|NUP54_uc011cbt.1_Intron|NUP54_uc003hjt.2_Intron	NM_017426	NP_059122			nucleoporin 54kDa						carbohydrate metabolic process|glucose transport|mRNA transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytoplasm|nuclear membrane|nuclear pore|nucleoplasm				ovary(1)|lung(1)	2																		---	---	---	---
SHROOM3	57619	broad.mit.edu	37	4	77615125	77615125	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77615125delA	uc011cbx.1	+						SHROOM3_uc011cbz.1_Intron	NM_020859	NP_065910			shroom family member 3 protein						apical protein localization|cell morphogenesis|cellular pigment accumulation|pattern specification process|regulation of cell shape	adherens junction|apical junction complex|apical plasma membrane|cytoplasm|microtubule	actin binding			skin(2)|ovary(1)	3			Lung(101;0.0903)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	78071183	78071183	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78071183delT								CCNI (74058 upstream) : CCNG2 (7174 downstream)																																			---	---	---	---
CCNG2	901	broad.mit.edu	37	4	78082886	78082886	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78082886delA	uc003hkq.3	+	6	994	c.691delA	c.(691-693)AAAfs	p.K231fs	CCNG2_uc003hkn.3_Frame_Shift_Del_p.K231fs|CCNG2_uc011ccc.1_Frame_Shift_Del_p.K231fs|CCNG2_uc003hkp.3_Frame_Shift_Del_p.K231fs	NM_004354	NP_004345	Q16589	CCNG2_HUMAN	cyclin G2	231					cell cycle checkpoint|cell division|mitosis	cytoplasm				ovary(2)|lung(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	78392225	78392225	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78392225delT								CCNG2 (301015 upstream) : CXCL13 (40682 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	80429846	80429846	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80429846delT	uc003hlv.2	+											Homo sapiens cDNA FLJ41919 fis, clone PERIC2002272.																														---	---	---	---
ANTXR2	118429	broad.mit.edu	37	4	80868611	80868611	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80868611delA	uc003hly.3	-						ANTXR2_uc003hlx.1_Intron	NM_058172	NP_477520			anthrax toxin receptor 2 isoform 1							endoplasmic reticulum membrane|extracellular region|integral to membrane|plasma membrane	metal ion binding|protein binding|receptor activity			ovary(1)	1														Juvenile_Hyaline_Fibromatosis				---	---	---	---
ANTXR2	118429	broad.mit.edu	37	4	80905931	80905933	+	Intron	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80905931_80905933delAAA	uc003hlz.3	-						ANTXR2_uc003hly.3_Intron|ANTXR2_uc003hlx.1_Intron|ANTXR2_uc010ijn.2_Intron	NM_001145794	NP_001139266			anthrax toxin receptor 2 isoform 2							endoplasmic reticulum membrane|extracellular region|integral to membrane|plasma membrane	metal ion binding|protein binding|receptor activity			ovary(1)	1														Juvenile_Hyaline_Fibromatosis				---	---	---	---
Unknown	0	broad.mit.edu	37	4	81243675	81243675	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81243675delT								FGF5 (31505 upstream) : C4orf22 (13199 downstream)																																			---	---	---	---
C4orf22	255119	broad.mit.edu	37	4	81626503	81626503	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81626503delT	uc003hmf.2	+						C4orf22_uc010ijp.2_Intron	NM_152770	NP_689983			hypothetical protein LOC255119											skin(2)	2																		---	---	---	---
C4orf22	255119	broad.mit.edu	37	4	81702987	81702988	+	Intron	DEL	AA	-	-	rs34486947	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81702987_81702988delAA	uc003hmf.2	+						C4orf22_uc010ijp.2_Intron	NM_152770	NP_689983			hypothetical protein LOC255119											skin(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	82280057	82280057	+	IGR	DEL	A	-	-	rs5859772		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82280057delA								PRKG2 (143839 upstream) : RASGEF1B (68162 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	84095373	84095373	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84095373delA								PLAC8 (59462 upstream) : COQ2 (87316 downstream)																																			---	---	---	---
HPSE	10855	broad.mit.edu	37	4	84241719	84241719	+	Intron	DEL	A	-	-	rs75657185		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84241719delA	uc003hoj.3	-						HPSE_uc010ika.2_Intron|HPSE_uc011ccq.1_Intron|HPSE_uc011ccr.1_Intron|HPSE_uc011ccs.1_Intron|HPSE_uc011cct.1_Intron|HPSE_uc003hok.3_Intron	NM_001098540	NP_001092010			heparanase precursor						carbohydrate metabolic process|cell adhesion|proteoglycan metabolic process	extracellular region|lysosomal membrane|nucleus	beta-glucuronidase activity|cation binding			ovary(1)	1		Hepatocellular(203;0.114)		COAD - Colon adenocarcinoma(81;0.141)	Heparin(DB01109)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	85003322	85003322	+	Intron	DEL	A	-	-	rs145808251		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85003322delA	uc010ikd.1	-						uc003hoz.1_Intron					Homo sapiens cDNA FLJ37966 fis, clone CTONG2009871.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	85010503	85010503	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85010503delA	uc010ikd.1	-						uc003hoz.1_Intron					Homo sapiens cDNA FLJ37966 fis, clone CTONG2009871.																														---	---	---	---
WDFY3	23001	broad.mit.edu	37	4	85674763	85674763	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85674763delA	uc003hpd.2	-							NM_014991	NP_055806			WD repeat and FYVE domain containing 3 isoform							cytoplasmic part|extrinsic to membrane|nuclear envelope	1-phosphatidylinositol binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)														---	---	---	---
ARHGAP24	83478	broad.mit.edu	37	4	86599195	86599195	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86599195delA	uc003hpk.2	+						ARHGAP24_uc003hpi.1_Intron|ARHGAP24_uc003hpj.2_Intron	NM_001025616	NP_001020787			Rho GTPase activating protein 24 isoform 1						angiogenesis|cell differentiation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell projection|cytoskeleton|cytosol|focal adhesion	GTPase activator activity|protein binding				0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)														---	---	---	---
MAPK10	5602	broad.mit.edu	37	4	86950967	86950968	+	Intron	DEL	TT	-	-	rs113679298		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86950967_86950968delTT	uc003hpq.2	-						MAPK10_uc010ikg.2_Intron|MAPK10_uc003hpr.2_Intron|MAPK10_uc003hps.2_Intron|MAPK10_uc003hpt.2_Intron|MAPK10_uc003hpu.2_Intron|MAPK10_uc003hpv.2_Intron|MAPK10_uc003hpn.2_Intron|MAPK10_uc003hpo.2_Intron|MAPK10_uc011ccw.1_Intron|MAPK10_uc003hpp.2_Intron	NM_138982	NP_620448			mitogen-activated protein kinase 10 isoform 2						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|JUN kinase activity|MAP kinase kinase activity|protein binding			stomach(1)|breast(1)|central_nervous_system(1)	3		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.243)		OV - Ovarian serous cystadenocarcinoma(123;0.002)														---	---	---	---
MAPK10	5602	broad.mit.edu	37	4	87066154	87066154	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87066154delA	uc003hpq.2	-						MAPK10_uc010ikg.2_Intron|MAPK10_uc003hpr.2_Intron|MAPK10_uc003hps.2_Intron|MAPK10_uc003hpt.2_Intron|MAPK10_uc003hpu.2_Intron|MAPK10_uc003hpv.2_Intron|MAPK10_uc010ikh.1_Intron|uc003hpw.2_Intron	NM_138982	NP_620448			mitogen-activated protein kinase 10 isoform 2						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|JUN kinase activity|MAP kinase kinase activity|protein binding			stomach(1)|breast(1)|central_nervous_system(1)	3		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.243)		OV - Ovarian serous cystadenocarcinoma(123;0.002)														---	---	---	---
MAPK10	5602	broad.mit.edu	37	4	87072377	87072377	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87072377delT	uc003hpq.2	-						MAPK10_uc010ikg.2_Intron|MAPK10_uc003hpr.2_Intron|MAPK10_uc003hps.2_Intron|MAPK10_uc003hpt.2_Intron|MAPK10_uc003hpu.2_Intron|MAPK10_uc003hpv.2_Intron|MAPK10_uc010ikh.1_Intron|uc003hpw.2_Intron	NM_138982	NP_620448			mitogen-activated protein kinase 10 isoform 2						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|JUN kinase activity|MAP kinase kinase activity|protein binding			stomach(1)|breast(1)|central_nervous_system(1)	3		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.243)		OV - Ovarian serous cystadenocarcinoma(123;0.002)														---	---	---	---
PTPN13	5783	broad.mit.edu	37	4	87612380	87612381	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87612380_87612381delAA	uc003hpz.2	+						PTPN13_uc003hpy.2_Intron|PTPN13_uc003hqa.2_Intron|PTPN13_uc003hqb.2_Intron	NM_080683	NP_542414			protein tyrosine phosphatase, non-receptor type							cytoplasm|cytoskeleton|plasma membrane	protein binding|protein binding|protein tyrosine phosphatase activity			ovary(4)|breast(1)|kidney(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)														---	---	---	---
PTPN13	5783	broad.mit.edu	37	4	87694134	87694134	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87694134delA	uc003hpz.2	+						PTPN13_uc003hpy.2_Intron|PTPN13_uc003hqa.2_Intron|PTPN13_uc003hqb.2_Intron|PTPN13_uc003hqc.1_Intron	NM_080683	NP_542414			protein tyrosine phosphatase, non-receptor type							cytoplasm|cytoskeleton|plasma membrane	protein binding|protein binding|protein tyrosine phosphatase activity			ovary(4)|breast(1)|kidney(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)														---	---	---	---
AFF1	4299	broad.mit.edu	37	4	87884953	87884954	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87884953_87884954delTT	uc011ccz.1	+						AFF1_uc011ccx.1_Intron|AFF1_uc003hqh.1_Intron|AFF1_uc011ccy.1_Intron	NM_005935	NP_005926			myeloid/lymphoid or mixed-lineage leukemia							nucleus	sequence-specific DNA binding transcription factor activity			breast(1)	1		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)														---	---	---	---
KLHL8	57563	broad.mit.edu	37	4	88095112	88095112	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88095112delT	uc011cdb.1	-						KLHL8_uc003hql.1_Intron|KLHL8_uc003hqm.1_Intron|KLHL8_uc003hqn.1_Intron|KLHL8_uc010ikj.1_Intron	NM_020803	NP_065854			kelch-like 8												0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)														---	---	---	---
HSD17B13	345275	broad.mit.edu	37	4	88226635	88226635	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88226635delT	uc003hqo.2	-						HSD17B13_uc010ikk.2_Intron	NM_178135	NP_835236			hydroxysteroid (17-beta) dehydrogenase 13							extracellular region	binding|oxidoreductase activity				0		Acute lymphoblastic leukemia(40;0.244)|all_hematologic(202;0.248)		OV - Ovarian serous cystadenocarcinoma(123;0.000308)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	88689122	88689122	+	IGR	DEL	T	-	-	rs4693180	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88689122delT								DMP1 (103612 upstream) : IBSP (31580 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	88690861	88690861	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88690861delT								DMP1 (105351 upstream) : IBSP (29841 downstream)																																			---	---	---	---
ABCG2	9429	broad.mit.edu	37	4	89015109	89015109	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89015109delT	uc003hrg.2	-						ABCG2_uc003hrh.2_Intron|ABCG2_uc003hrf.2_Intron	NM_004827	NP_004818			ATP-binding cassette, sub-family G, member 2						cellular iron ion homeostasis|urate metabolic process	integral to membrane|plasma membrane	ATP binding|heme transporter activity|protein homodimerization activity|xenobiotic-transporting ATPase activity			central_nervous_system(1)	1		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.02e-05)	Imatinib(DB00619)|Mitoxantrone(DB01204)|Nicardipine(DB00622)|Nitrendipine(DB01054)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Topotecan(DB01030)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	89168994	89168995	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89168994_89168995delTT								ABCG2 (16520 upstream) : PPM1K (12539 downstream)																																			---	---	---	---
HERC5	51191	broad.mit.edu	37	4	89426755	89426755	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89426755delT	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	89545340	89545340	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89545340delC	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	89558118	89558119	+	Intron	INS	-	AA	AA			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89558118_89558119insAA	uc003hrw.1	+						HERC3_uc003hrv.2_Intron|HERC3_uc011cdn.1_Intron	NM_014606	NP_055421			hect domain and RLD 3						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasmic membrane-bounded vesicle	ubiquitin-protein ligase activity			lung(2)|prostate(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(123;0.000319)														---	---	---	---
FAM13A	10144	broad.mit.edu	37	4	89651553	89651554	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89651553_89651554insT	uc003hse.1	-						FAM13A_uc011cdp.1_Intron|FAM13A_uc003hsa.1_Intron|FAM13A_uc003hsb.1_Intron|FAM13A_uc003hsd.1_Intron|FAM13A_uc003hsc.1_Intron|FAM13A_uc011cdq.1_Intron|FAM13A_uc003hsf.1_Intron	NM_014883	NP_055698			family with sequence similarity 13, member A1						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(1)|liver(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	90334252	90334253	+	IGR	INS	-	A	A	rs142295907	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90334252_90334253insA								GPRIN3 (105091 upstream) : SNCA (310998 downstream)																																			---	---	---	---
FAM190A	401145	broad.mit.edu	37	4	91663243	91663244	+	Intron	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91663243_91663244delAG	uc003hsv.3	+						FAM190A_uc010ikv.2_Intron|FAM190A_uc003hsw.2_Intron|FAM190A_uc003hsx.2_Intron	NM_001145065	NP_001138537			KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2																		---	---	---	---
FAM190A	401145	broad.mit.edu	37	4	92066452	92066452	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:92066452delT	uc003hsv.3	+							NM_001145065	NP_001138537			KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	92565215	92565215	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:92565215delA								FAM190A (41846 upstream) : GRID2 (660335 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	93205572	93205572	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:93205572delT								FAM190A (682203 upstream) : GRID2 (19978 downstream)																																			---	---	---	---
GRID2	2895	broad.mit.edu	37	4	93925374	93925374	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:93925374delT	uc011cdt.1	+						GRID2_uc010ikx.2_Intron|GRID2_uc011cdu.1_Intron|GRID2_uc011cdv.1_Intron	NM_001510	NP_001501			glutamate receptor, ionotropic, delta 2						glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)													---	---	---	---
GRID2	2895	broad.mit.edu	37	4	94583285	94583285	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94583285delT	uc011cdt.1	+						GRID2_uc011cdu.1_Intron	NM_001510	NP_001501			glutamate receptor, ionotropic, delta 2						glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)													---	---	---	---
GRID2	2895	broad.mit.edu	37	4	94678366	94678366	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94678366delA	uc011cdt.1	+						GRID2_uc011cdu.1_Intron	NM_001510	NP_001501			glutamate receptor, ionotropic, delta 2						glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)													---	---	---	---
SMARCAD1	56916	broad.mit.edu	37	4	95204462	95204462	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95204462delT	uc003htc.3	+						SMARCAD1_uc003htb.3_Intron|SMARCAD1_uc003htd.3_Intron|SMARCAD1_uc010ila.2_Intron|SMARCAD1_uc011cdw.1_Intron	NM_020159	NP_064544			SWI/SNF-related, matrix-associated						chromatin modification|nucleotide metabolic process|positive regulation of transcription, DNA-dependent|protein homooligomerization|regulation of DNA recombination	nuclear matrix	ATP binding|DNA binding|helicase activity			skin(2)|ovary(1)|breast(1)	4				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)														---	---	---	---
PDLIM5	10611	broad.mit.edu	37	4	95396297	95396297	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95396297delT	uc003hti.2	+						PDLIM5_uc003htf.2_Intron|PDLIM5_uc003htg.2_Intron|PDLIM5_uc011cdx.1_Intron|PDLIM5_uc003hth.2_Intron|PDLIM5_uc003htj.2_Intron|PDLIM5_uc003htk.2_Intron|PDLIM5_uc011cdy.1_Intron	NM_006457	NP_006448			PDZ and LIM domain 5 isoform a						regulation of dendritic spine morphogenesis|regulation of synaptogenesis	actin cytoskeleton|cell junction|cytosol|postsynaptic density|postsynaptic membrane|synaptosome	actin binding|actinin binding|protein kinase C binding|zinc ion binding			ovary(1)|skin(1)	2		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.84e-09)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	95638971	95638974	+	IGR	DEL	AAAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95638971_95638974delAAAA								PDLIM5 (49595 upstream) : BMPR1B (40154 downstream)																																			---	---	---	---
BMPR1B	658	broad.mit.edu	37	4	95933191	95933191	+	Intron	DEL	A	-	-	rs76517516		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95933191delA	uc003htm.3	+							NM_001203	NP_001194			bone morphogenetic protein receptor, type IB						BMP signaling pathway|cartilage condensation|eye development|limb morphogenesis|ovarian cumulus expansion|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	receptor complex	ATP binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta receptor activity			lung(4)|skin(2)|stomach(1)|breast(1)	8		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.51e-07)														---	---	---	---
UNC5C	8633	broad.mit.edu	37	4	96315802	96315803	+	Intron	INS	-	TGTG	TGTG	rs148901088	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96315802_96315803insTGTG	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	98016275	98016275	+	IGR	DEL	A	-	-	rs146327926	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:98016275delA								None (None upstream) : C4orf37 (463759 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	98226571	98226571	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:98226571delA								None (None upstream) : C4orf37 (253463 downstream)																																			---	---	---	---
METAP1	23173	broad.mit.edu	37	4	99960367	99960367	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99960367delT	uc003huf.3	+						METAP1_uc003hug.2_Intron	NM_015143	NP_055958			methionyl aminopeptidase 1						N-terminal protein amino acid modification|peptidyl-methionine modification|proteolysis|regulation of translation	cytoplasm	aminopeptidase activity|metal ion binding|metalloexopeptidase activity|protein binding				0				OV - Ovarian serous cystadenocarcinoma(123;3.12e-07)														---	---	---	---
ADH5	128	broad.mit.edu	37	4	99996373	99996373	+	Intron	DEL	G	-	-	rs71600256		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99996373delG	uc003hui.2	-						ADH5_uc003huj.2_Intron	NM_000671	NP_000662			class III alcohol dehydrogenase, chi subunit						ethanol oxidation|response to redox state		alcohol dehydrogenase (NAD) activity|electron carrier activity|fatty acid binding|formaldehyde dehydrogenase activity|S-(hydroxymethyl)glutathione dehydrogenase activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(123;2.5e-07)	NADH(DB00157)													---	---	---	---
ADH6	130	broad.mit.edu	37	4	100125814	100125814	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100125814delA	uc003huo.2	-						uc003hum.1_Intron|ADH6_uc011cef.1_Intron	NM_001102470	NP_001095940			class V alcohol dehydrogenase isoform 1						ethanol oxidation|response to ethanol|xenobiotic metabolic process	cytosol	alcohol dehydrogenase (NAD) activity|electron carrier activity|zinc ion binding			ovary(1)|kidney(1)|skin(1)	3				OV - Ovarian serous cystadenocarcinoma(123;3.58e-08)	Abacavir(DB01048)|NADH(DB00157)													---	---	---	---
ADH1A	124	broad.mit.edu	37	4	100226148	100226149	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100226148_100226149delTT	uc011ceg.1	-							NM_000667	NP_000658			class I alcohol dehydrogenase, alpha subunit						ethanol oxidation|transcription, DNA-dependent|xenobiotic metabolic process	cytosol	alcohol dehydrogenase activity, zinc-dependent|protein binding|zinc ion binding			large_intestine(1)|ovary(1)	2				OV - Ovarian serous cystadenocarcinoma(123;9.56e-08)	Fomepizole(DB01213)|NADH(DB00157)													---	---	---	---
RG9MTD2	93587	broad.mit.edu	37	4	100477696	100477696	+	Intron	DEL	T	-	-	rs67490132		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100477696delT	uc003huy.2	-						RG9MTD2_uc003huz.3_Intron|RG9MTD2_uc003hva.3_Intron	NM_152292	NP_689505			RNA (guanine-9-) methyltransferase domain								methyltransferase activity			ovary(2)|breast(1)	3				OV - Ovarian serous cystadenocarcinoma(123;1.7e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	101061869	101061870	+	IGR	DEL	TT	-	-	rs71594572		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:101061869_101061870delTT								LOC256880 (188249 upstream) : DDIT4L (45159 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	101295822	101295822	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:101295822delT								DDIT4L (184209 upstream) : EMCN (20678 downstream)																																			---	---	---	---
EMCN	51705	broad.mit.edu	37	4	101333108	101333108	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:101333108delT	uc003hvr.2	-						EMCN_uc011cel.1_Intron|EMCN_uc011cem.1_Intron	NM_016242	NP_057326			endomucin isoform 1							extracellular region|integral to membrane|plasma membrane					0				OV - Ovarian serous cystadenocarcinoma(123;2.49e-08)														---	---	---	---
SLC39A8	64116	broad.mit.edu	37	4	103195359	103195359	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103195359delA	uc003hwb.1	-						SLC39A8_uc011ceo.1_Intron|SLC39A8_uc003hwa.1_Intron|SLC39A8_uc003hwc.2_Intron	NM_022154	NP_071437			solute carrier family 39 (zinc transporter),							integral to membrane|organelle membrane|plasma membrane	zinc ion transmembrane transporter activity				0		Hepatocellular(203;0.217)		all cancers(1;9.78e-10)|OV - Ovarian serous cystadenocarcinoma(123;1.52e-09)|GBM - Glioblastoma multiforme(1;0.000142)														---	---	---	---
MANBA	4126	broad.mit.edu	37	4	103609543	103609544	+	Intron	INS	-	AC	AC	rs139735718	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103609543_103609544insAC	uc003hwg.2	-						MANBA_uc011ces.1_Intron	NM_005908	NP_005899			mannosidase, beta A, lysosomal precursor						carbohydrate metabolic process|protein modification process	lysosome	beta-mannosidase activity|cation binding			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;4.44e-08)														---	---	---	---
UBE2D3	7323	broad.mit.edu	37	4	103718308	103718308	+	3'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103718308delT	uc003hwk.2	-	8					UBE2D3_uc003hwh.2_5'Flank|UBE2D3_uc003hwi.2_3'UTR|UBE2D3_uc003hwj.2_RNA|UBE2D3_uc003hwl.2_3'UTR|UBE2D3_uc011cet.1_3'UTR|UBE2D3_uc011ceu.1_3'UTR|UBE2D3_uc003hwo.2_3'UTR|UBE2D3_uc003hwp.2_3'UTR|UBE2D3_uc003hwq.2_3'UTR|UBE2D3_uc003hwr.2_3'UTR	NM_181887	NP_871616			ubiquitin-conjugating enzyme E2D 3 isoform 1						apoptosis|BMP signaling pathway|DNA repair|negative regulation of type I interferon production|proteasomal ubiquitin-dependent protein catabolic process|protein K11-linked ubiquitination|protein K48-linked ubiquitination|protein monoubiquitination|transforming growth factor beta receptor signaling pathway	endosome membrane|plasma membrane	ATP binding|protein binding|ubiquitin-protein ligase activity				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.13e-08)														---	---	---	---
UBE2D3	7323	broad.mit.edu	37	4	103720344	103720344	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103720344delA	uc003hwk.2	-						UBE2D3_uc003hwi.2_Intron|UBE2D3_uc003hwj.2_Intron|UBE2D3_uc003hwl.2_Intron|UBE2D3_uc011cet.1_Intron|UBE2D3_uc011ceu.1_Intron|UBE2D3_uc003hwo.2_Intron|UBE2D3_uc003hwp.2_Intron|UBE2D3_uc003hwq.2_Intron|UBE2D3_uc003hwr.2_Intron	NM_181887	NP_871616			ubiquitin-conjugating enzyme E2D 3 isoform 1						apoptosis|BMP signaling pathway|DNA repair|negative regulation of type I interferon production|proteasomal ubiquitin-dependent protein catabolic process|protein K11-linked ubiquitination|protein K48-linked ubiquitination|protein monoubiquitination|transforming growth factor beta receptor signaling pathway	endosome membrane|plasma membrane	ATP binding|protein binding|ubiquitin-protein ligase activity				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.13e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	104283525	104283526	+	IGR	INS	-	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104283525_104283526insC								CENPE (163959 upstream) : TACR3 (227099 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	104343296	104343296	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104343296delT								CENPE (223730 upstream) : TACR3 (167329 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	105509265	105509265	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:105509265delT	uc003hxh.1	+											Homo sapiens cDNA FLJ37242 fis, clone BRAMY2004335.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	105778684	105778684	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:105778684delG								CXXC4 (362626 upstream) : TET2 (289259 downstream)																																			---	---	---	---
PPA2	27068	broad.mit.edu	37	4	106332427	106332428	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106332427_106332428insA	uc003hxl.2	-						PPA2_uc003hxm.2_Intron|PPA2_uc003hxn.2_Intron|PPA2_uc003hxo.2_Intron|PPA2_uc003hxp.2_Intron|PPA2_uc003hxq.2_Intron|PPA2_uc003hxr.2_Intron|PPA2_uc011cfa.1_Intron	NM_176869	NP_789845			inorganic pyrophosphatase 2 isoform 1 precursor						diphosphate metabolic process|tRNA aminoacylation for protein translation	mitochondrial matrix	inorganic diphosphatase activity|magnesium ion binding			pancreas(1)	1		Myeloproliferative disorder(5;0.0255)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.03e-07)														---	---	---	---
GSTCD	79807	broad.mit.edu	37	4	106718203	106718204	+	Intron	INS	-	TGTGTG	TGTGTG	rs28533186		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106718203_106718204insTGTGTG	uc003hxz.3	+						GSTCD_uc003hxx.2_Intron|GSTCD_uc003hxy.3_Intron|GSTCD_uc011cfb.1_Intron	NM_001031720	NP_001026890			glutathione S-transferase, C-terminal domain							cytoplasm	rRNA methyltransferase activity			breast(1)|central_nervous_system(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.15e-07)|READ - Rectum adenocarcinoma(30;0.139)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	107270997	107270998	+	IGR	INS	-	AACA	AACA	rs138729397	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107270997_107270998insAACA								AIMP1 (618 upstream) : DKK2 (571962 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	107403729	107403729	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107403729delT								AIMP1 (133350 upstream) : DKK2 (439231 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	107814545	107814545	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107814545delC								AIMP1 (544166 upstream) : DKK2 (28415 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	108492104	108492104	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108492104delT								DKK2 (287258 upstream) : PAPSS1 (42719 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	109114862	109114862	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109114862delA								LEF1 (25284 upstream) : LOC285456 (344484 downstream)																																			---	---	---	---
COL25A1	84570	broad.mit.edu	37	4	109984700	109984700	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109984700delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	111232063	111232063	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111232063delA								ELOVL6 (112243 upstream) : ENPEP (165166 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	112450058	112450058	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:112450058delT								MIR297 (668255 upstream) : C4orf32 (616495 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	112731409	112731410	+	IGR	DEL	AA	-	-	rs77800861		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:112731409_112731410delAA								MIR297 (949606 upstream) : C4orf32 (335143 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	112906594	112906594	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:112906594delA								None (None upstream) : C4orf32 (159959 downstream)																																			---	---	---	---
ALPK1	80216	broad.mit.edu	37	4	113335765	113335765	+	Intron	DEL	A	-	-	rs115042080		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113335765delA	uc003iap.3	+						ALPK1_uc011cfw.1_Intron|ALPK1_uc003ian.3_Intron|ALPK1_uc011cfx.1_Intron|ALPK1_uc003iao.3_Intron|ALPK1_uc003iaq.2_3'UTR|ALPK1_uc010imo.2_Intron|ALPK1_uc003iar.2_3'UTR	NM_025144	NP_079420			alpha-kinase 1								ATP binding|protein serine/threonine kinase activity			ovary(5)	5		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)														---	---	---	---
ANK2	287	broad.mit.edu	37	4	114199851	114199851	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114199851delT	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)												OREG0016024	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ANK2	287	broad.mit.edu	37	4	114289147	114289148	+	Intron	DEL	AA	-	-	rs55966162	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114289147_114289148delAA	uc003ibe.3	+						ANK2_uc003ibd.3_Intron|ANK2_uc003ibf.3_Intron|ANK2_uc011cgc.1_Intron|ANK2_uc003ibg.3_Intron|ANK2_uc003ibh.3_Intron|ANK2_uc011cgd.1_Intron	NM_001148	NP_001139			ankyrin 2 isoform 1						axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)|skin(1)	14		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)														---	---	---	---
ANK2	287	broad.mit.edu	37	4	114300948	114300948	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114300948delA	uc003ibe.3	+						ANK2_uc003ibd.3_Intron|ANK2_uc003ibf.3_Intron|ANK2_uc011cgc.1_Intron|ANK2_uc003ibg.3_Intron|ANK2_uc003ibh.3_Intron|ANK2_uc011cgd.1_Intron|ANK2_uc010imr.2_Intron|ANK2_uc010ims.2_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	114665003	114665004	+	Intron	DEL	TT	-	-	rs11383083		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114665003_114665004delTT	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	115125044	115125044	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115125044delT								ARSJ (224166 upstream) : UGT8 (394567 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	115431962	115431962	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115431962delT								ARSJ (531084 upstream) : UGT8 (87649 downstream)																																			---	---	---	---
NDST4	64579	broad.mit.edu	37	4	115799113	115799113	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115799113delA	uc003ibu.2	-						NDST4_uc010imw.2_Intron	NM_022569	NP_072091			heparan sulfate N-deacetylase/N-sulfotransferase							Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			skin(3)|ovary(1)	4		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	116295144	116295144	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:116295144delT								NDST4 (260112 upstream) : MIR1973 (925737 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	117062297	117062298	+	IGR	DEL	TA	-	-	rs145597636		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:117062297_117062298delTA								None (None upstream) : MIR1973 (158583 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	117536458	117536459	+	IGR	INS	-	GAAG	GAAG	rs148365262	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:117536458_117536459insGAAG								MIR1973 (315534 upstream) : TRAM1L1 (468257 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	118554667	118554667	+	IGR	DEL	T	-	-	rs33943988		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:118554667delT								TRAM1L1 (547931 upstream) : NDST3 (400106 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	118671918	118671918	+	IGR	DEL	A	-	-	rs33939855		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:118671918delA								TRAM1L1 (665182 upstream) : NDST3 (282855 downstream)																																			---	---	---	---
NDST3	9348	broad.mit.edu	37	4	119178295	119178295	+	3'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119178295delT	uc003ibx.2	+	14						NM_004784	NP_004775			N-deacetylase/N-sulfotransferase (heparan							Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			large_intestine(1)	1																		---	---	---	---
SEC24D	9871	broad.mit.edu	37	4	119659245	119659245	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119659245delA	uc003ici.3	-						SEC24D_uc003ich.3_Intron|SEC24D_uc003icj.3_Intron|SEC24D_uc003icl.2_Intron	NM_014822	NP_055637			Sec24-related protein D						COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	zinc ion binding				0																		---	---	---	---
PRDM5	11107	broad.mit.edu	37	4	121616101	121616101	+	3'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:121616101delT	uc003idn.2	-	16					PRDM5_uc003ido.2_3'UTR|PRDM5_uc010ine.2_3'UTR	NM_018699	NP_061169			PR domain containing 5						histone deacetylation|histone H3-K9 methylation|mitotic cell cycle|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	repressing transcription factor binding|sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding			central_nervous_system(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	121879122	121879122	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:121879122delT								PRDM5 (35109 upstream) : C4orf31 (77660 downstream)																																			---	---	---	---
ANXA5	308	broad.mit.edu	37	4	122605168	122605168	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122605168delA	uc003idu.3	-						ANXA5_uc003idv.3_Intron|ANXA5_uc003idw.3_Intron|ANXA5_uc010inm.2_Intron|ANXA5_uc010inn.2_Intron|ANXA5_uc010ino.2_Intron	NM_001154	NP_001145			annexin 5						anti-apoptosis|blood coagulation|negative regulation of coagulation|signal transduction	cytoplasm	calcium ion binding|calcium-dependent phospholipid binding|phospholipase inhibitor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	122692306	122692307	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122692306_122692307delTT								LOC100192379 (4344 upstream) : EXOSC9 (30165 downstream)																																			---	---	---	---
EXOSC9	5393	broad.mit.edu	37	4	122723206	122723206	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122723206delT	uc003iea.2	+						EXOSC9_uc003idz.2_Intron|EXOSC9_uc003ieb.2_Intron|EXOSC9_uc010inp.1_5'Flank	NM_005033	NP_005024			exosome component 9 isoform 2						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|immune response|nuclear mRNA surveillance|nuclear polyadenylation-dependent rRNA catabolic process|positive regulation of cell growth|rRNA processing	cytosol|nuclear exosome (RNase complex)|nucleolus|nucleolus|nucleus	3'-5'-exoribonuclease activity|AU-rich element binding|protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	123038801	123038801	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123038801delA								TRPC3 (165892 upstream) : KIAA1109 (52957 downstream)																																			---	---	---	---
ADAD1	132612	broad.mit.edu	37	4	123316820	123316822	+	Intron	DEL	AAA	-	-	rs80027649		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123316820_123316822delAAA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	123533753	123533754	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123533753_123533754insT								IL2 (156103 upstream) : IL21 (29 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	124308441	124308441	+	IGR	DEL	A	-	-	rs75815322		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:124308441delA								SPATA5 (67839 upstream) : SPRY1 (9515 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	124561525	124561525	+	IGR	DEL	T	-	-	rs79747824		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:124561525delT								SPRY1 (236618 upstream) : LOC285419 (9897 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	125661419	125661419	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125661419delA								ANKRD50 (27532 upstream) : FAT4 (576148 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	126719117	126719118	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126719117_126719118insA								MIR2054 (290655 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	127400878	127400878	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:127400878delT								MIR2054 (972416 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	127597809	127597809	+	IGR	DEL	C	-	-	rs66537262		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:127597809delC								None (None upstream) : INTU (956311 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	128023598	128023599	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128023598_128023599delTG								None (None upstream) : INTU (530521 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	128114584	128114584	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128114584delT								None (None upstream) : INTU (439536 downstream)																																			---	---	---	---
HSPA4L	22824	broad.mit.edu	37	4	128722470	128722470	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128722470delT	uc003ifm.2	+						HSPA4L_uc010iny.1_Intron|HSPA4L_uc011cgr.1_Intron	NM_014278	NP_055093			heat shock 70kDa protein 4-like						protein folding|response to unfolded protein	cytoplasm|nucleus	ATP binding|protein binding			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
HSPA4L	22824	broad.mit.edu	37	4	128724724	128724724	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128724724delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	128781008	128781009	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128781008_128781009delAA								HSPA4L (26486 upstream) : PLK4 (21036 downstream)																																			---	---	---	---
LARP1B	55132	broad.mit.edu	37	4	129117449	129117451	+	Intron	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129117449_129117451delAAA	uc003iga.2	+						LARP1B_uc003igc.2_Intron|LARP1B_uc010ioa.1_Intron|LARP1B_uc003ige.2_Intron|LARP1B_uc003igd.2_Intron	NM_018078	NP_060548			La ribonucleoprotein domain family member 2								RNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	129235585	129235585	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129235585delT								PGRMC2 (26637 upstream) : PHF17 (495194 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	129541832	129541835	+	IGR	DEL	AAAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129541832_129541835delAAAA								PGRMC2 (332884 upstream) : PHF17 (188944 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	129664269	129664269	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129664269delA								PGRMC2 (455321 upstream) : PHF17 (66510 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	130078380	130078380	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:130078380delA								C4orf33 (44538 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	130125417	130125419	+	IGR	DEL	ACA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:130125417_130125419delACA								C4orf33 (91575 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	130344410	130344410	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:130344410delT								C4orf33 (310568 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	130669398	130669398	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:130669398delT	uc003igv.2	-											Homo sapiens cDNA clone IMAGE:5265890.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	131137361	131137361	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:131137361delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	131429211	131429211	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:131429211delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	133192578	133192579	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:133192578_133192579delTG								None (None upstream) : PCDH10 (877891 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	136105667	136105667	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:136105667delA								PABPC4L (982764 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	136857482	136857483	+	IGR	INS	-	CTTA	CTTA	rs148700506	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:136857482_136857483insCTTA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	138062414	138062414	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:138062414delA								None (None upstream) : PCDH18 (377662 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	138236716	138236719	+	IGR	DEL	GTTG	-	-	rs71598386		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:138236716_138236719delGTTG								None (None upstream) : PCDH18 (203357 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	138275002	138275002	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:138275002delT								None (None upstream) : PCDH18 (165074 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	138821648	138821648	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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	139867056	139867056	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139867056delA								SLC7A11 (703553 upstream) : CCRN4L (69887 downstream)																																			---	---	---	---
ELF2	1998	broad.mit.edu	37	4	140037518	140037519	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140037518_140037519delAA	uc003ihp.1	-						ELF2_uc003ihq.2_Intron	NM_201999	NP_973728			E74-like factor 2 (ets domain transcription						negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter	cytoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2	all_hematologic(180;0.162)																	---	---	---	---
ELF2	1998	broad.mit.edu	37	4	140051373	140051374	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140051373_140051374insA	uc003ihp.1	-						ELF2_uc003ihq.2_Intron	NM_201999	NP_973728			E74-like factor 2 (ets domain transcription						negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter	cytoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2	all_hematologic(180;0.162)																	---	---	---	---
C4orf49	84709	broad.mit.edu	37	4	140188339	140188339	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140188339delA	uc003ihr.1	-							NM_032623	NP_116012			ovary-specific acidic protein							integral to membrane				central_nervous_system(1)|skin(1)	2																		---	---	---	---
MAML3	55534	broad.mit.edu	37	4	140882856	140882856	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140882856delA	uc003ihz.1	-						MAML3_uc011chd.1_Intron	NM_018717	NP_061187			mastermind-like 3						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity			ovary(1)	1	all_hematologic(180;0.162)																	---	---	---	---
MAML3	55534	broad.mit.edu	37	4	141029006	141029006	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141029006delA	uc003ihz.1	-						MAML3_uc011chd.1_Intron	NM_018717	NP_061187			mastermind-like 3						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity			ovary(1)	1	all_hematologic(180;0.162)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	142444083	142444083	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142444083delA								ZNF330 (288235 upstream) : IL15 (113671 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	142524072	142524072	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142524072delT								ZNF330 (368224 upstream) : IL15 (33682 downstream)																																			---	---	---	---
INPP4B	8821	broad.mit.edu	37	4	143043165	143043165	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143043165delA	uc003iix.3	-						INPP4B_uc003iiw.3_Intron|INPP4B_uc011chm.1_Intron|INPP4B_uc011chn.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	143053422	143053422	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143053422delT	uc003iix.3	-						INPP4B_uc003iiw.3_Intron|INPP4B_uc011chm.1_Intron|INPP4B_uc011chn.1_Intron|INPP4B_uc011cho.1_Intron|INPP4B_uc011chp.1_Intron	NM_003866	NP_003857			inositol polyphosphate-4-phosphatase, type II,						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	144194721	144194721	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144194721delA								USP38 (51581 upstream) : GAB1 (63262 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	144235153	144235153	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144235153delA								USP38 (92013 upstream) : GAB1 (22830 downstream)																																			---	---	---	---
GAB1	2549	broad.mit.edu	37	4	144373454	144373455	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144373454_144373455insT	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	145456051	145456052	+	IGR	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145456051_145456052delGT								GYPA (394147 upstream) : HHIP (111121 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	146262661	146262661	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146262661delA								OTUD4 (161829 upstream) : SMAD1 (140290 downstream)																																			---	---	---	---
MMAA	166785	broad.mit.edu	37	4	146542745	146542745	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146542745delG	uc003ikh.3	+						MMAA_uc003ikg.2_Intron	NM_172250	NP_758454			methylmalonic aciduria type A precursor							mitochondrion	GTP binding|nucleoside-triphosphatase activity			ovary(1)	1	all_hematologic(180;0.151)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	146950481	146950481	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146950481delT								ZNF827 (90874 upstream) : LSM6 (146354 downstream)																																			---	---	---	---
SLC10A7	84068	broad.mit.edu	37	4	147325629	147325636	+	Intron	DEL	TGTGTGTG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147325629_147325636delTGTGTGTG	uc010ioz.2	-						SLC10A7_uc003ikr.2_Intron|SLC10A7_uc010ipa.2_Intron|SLC10A7_uc003iks.2_Intron	NM_001029998	NP_001025169			solute carrier family 10 (sodium/bile acid							integral to membrane	bile acid:sodium symporter activity				0	all_hematologic(180;0.151)																	---	---	---	---
SLC10A7	84068	broad.mit.edu	37	4	147413998	147413998	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147413998delT	uc010ioz.2	-						SLC10A7_uc003ikr.2_Intron|SLC10A7_uc010ipa.2_Intron|SLC10A7_uc003iks.2_Intron|SLC10A7_uc003ikt.2_Intron	NM_001029998	NP_001025169			solute carrier family 10 (sodium/bile acid							integral to membrane	bile acid:sodium symporter activity				0	all_hematologic(180;0.151)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	147992185	147992185	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147992185delT								TTC29 (125151 upstream) : MIR548G (273596 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	148518780	148518780	+	IGR	DEL	A	-	-	rs11301239		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148518780delA								EDNRA (52674 upstream) : TMEM184C (19759 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	149955918	149955918	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149955918delT								NR3C2 (592275 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	150255574	150255575	+	IGR	INS	-	TG	TG	rs142038287	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:150255574_150255575insTG								NR3C2 (891931 upstream) : DCLK2 (744505 downstream)																																			---	---	---	---
DCLK2	166614	broad.mit.edu	37	4	151102775	151102777	+	Intron	DEL	TTA	-	-	rs6535717	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151102775_151102777delTTA	uc003ilm.3	+						DCLK2_uc003iln.3_Intron|DCLK2_uc003ilo.3_Intron|DCLK2_uc003ilp.3_Intron	NM_001040260	NP_001035350			doublecortin-like kinase 2 isoform a						intracellular signal transduction	cytoplasm|cytoskeleton	ATP binding|protein serine/threonine kinase activity			ovary(3)	3	all_hematologic(180;0.151)																	---	---	---	---
RPS3A	6189	broad.mit.edu	37	4	152022581	152022581	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152022581delT	uc003ilz.2	+						RPS3A_uc011cie.1_Intron|SNORD73A_uc003ima.1_5'Flank	NM_001006	NP_000997			ribosomal protein S3a						cell differentiation|endocrine pancreas development|induction of apoptosis|translational elongation|translational initiation|translational termination|viral transcription	cytosolic small ribosomal subunit|nucleolus	protein binding|RNA binding|structural constituent of ribosome			ovary(1)	1	all_hematologic(180;0.093)																	---	---	---	---
SH3D19	152503	broad.mit.edu	37	4	152056459	152056459	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152056459delA	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	152145465	152145465	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152145465delA	uc010ipl.1	-						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)																---	---	---	---
PRSS48	345062	broad.mit.edu	37	4	152204057	152204057	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152204057delA	uc011cif.1	+						PRSS48_uc011cig.1_Intron	NM_183375	NP_899231			epidermis-specific serine protease-like protein						proteolysis	extracellular region	serine-type endopeptidase activity			large_intestine(1)	1																		---	---	---	---
FAM160A1	729830	broad.mit.edu	37	4	152503507	152503508	+	Intron	DEL	TT	-	-	rs74414311		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152503507_152503508delTT	uc003imj.2	+							NM_001109977	NP_001103447			hypothetical protein LOC729830												0																		---	---	---	---
FBXW7	55294	broad.mit.edu	37	4	153429228	153429228	+	Intron	DEL	A	-	-	rs113719352		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153429228delA	uc003ims.2	-						FBXW7_uc011cii.1_Intron|FBXW7_uc003imt.2_Intron|FBXW7_uc003imu.2_Intron	NM_033632	NP_361014			F-box and WD repeat domain containing 7 isoform						interspecies interaction between organisms|lipid homeostasis|negative regulation of DNA endoreduplication|negative regulation of hepatocyte proliferation|negative regulation of Notch signaling pathway|negative regulation of triglyceride biosynthetic process|positive regulation of epidermal growth factor receptor activity|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|protein ubiquitination|regulation of lipid storage|regulation of protein localization|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|sister chromatid cohesion|vasculature development	nucleolus|nucleolus|nucleoplasm|nucleoplasm|SCF ubiquitin ligase complex	protein binding|protein binding			haematopoietic_and_lymphoid_tissue(125)|large_intestine(99)|stomach(16)|lung(14)|endometrium(13)|ovary(9)|biliary_tract(8)|upper_aerodigestive_tract(5)|central_nervous_system(3)|kidney(3)|skin(3)|pancreas(3)|breast(2)|prostate(2)|cervix(1)|NS(1)|bone(1)	308	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)						Mis|N|D|F		colorectal|endometrial|T-ALL								---	---	---	---
TRIM2	23321	broad.mit.edu	37	4	154098799	154098799	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154098799delA	uc003ing.2	+							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	154160571	154160572	+	Intron	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154160571_154160572delCT	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	154591345	154591347	+	IGR	DEL	TTT	-	-	rs76681902		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154591345_154591347delTTT								KIAA0922 (33485 upstream) : TLR2 (14094 downstream)																																			---	---	---	---
RNF175	285533	broad.mit.edu	37	4	154649262	154649262	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154649262delC	uc003int.2	-						RNF175_uc003inu.1_Intron	NM_173662	NP_775933			ring finger protein 175							integral to membrane	zinc ion binding			ovary(1)|pancreas(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)																---	---	---	---
RNF175	285533	broad.mit.edu	37	4	154679927	154679928	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154679927_154679928delAA	uc003int.2	-						RNF175_uc003inu.1_Intron	NM_173662	NP_775933			ring finger protein 175							integral to membrane	zinc ion binding			ovary(1)|pancreas(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)																---	---	---	---
DCHS2	54798	broad.mit.edu	37	4	155410049	155410054	+	Intron	DEL	TGTGTC	-	-	rs67739831		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155410049_155410054delTGTGTC	uc003inx.2	-						DCHS2_uc011cik.1_Intron	NM_001142552	NP_001136024			dachsous 2 isoform 2						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	155584691	155584691	+	Intron	DEL	T	-	-	rs34115626		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155584691delT	uc003iol.2	+											Homo sapiens cDNA FLJ31672 fis, clone NT2RI2005048.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	155874952	155874952	+	IGR	DEL	A	-	-	rs112304427		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155874952delA								RBM46 (124988 upstream) : NPY2R (254829 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	157986879	157986879	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157986879delT								PDGFC (94333 upstream) : GLRB (10398 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	158563698	158563699	+	IGR	DEL	TG	-	-	rs34627989		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158563698_158563699delTG								LOC340017 (66403 upstream) : FAM198B (482034 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	158706575	158706576	+	IGR	DEL	AT	-	-	rs1585958	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158706575_158706576delAT								LOC340017 (209280 upstream) : FAM198B (339157 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	159391193	159391198	+	IGR	DEL	CTTTAG	-	-	rs138795576	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159391193_159391198delCTTTAG								TMEM144 (214755 upstream) : RXFP1 (51849 downstream)																																			---	---	---	---
RAPGEF2	9693	broad.mit.edu	37	4	160260638	160260638	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160260638delT	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	161139924	161139925	+	IGR	INS	-	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:161139924_161139925insC								RAPGEF2 (858625 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	161329032	161329032	+	IGR	DEL	T	-	-	rs78382298		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:161329032delT								None (None upstream) : FSTL5 (976019 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	162041827	162041828	+	IGR	DEL	AA	-	-	rs34457360		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:162041827_162041828delAA								None (None upstream) : FSTL5 (263223 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	162073286	162073287	+	IGR	DEL	GC	-	-	rs6830631	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:162073286_162073287delGC								None (None upstream) : FSTL5 (231764 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	163180513	163180514	+	IGR	INS	-	TG	TG	rs142303835	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:163180513_163180514insTG								FSTL5 (95327 upstream) : NAF1 (867346 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	163453538	163453539	+	IGR	INS	-	CA	CA			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:163453538_163453539insCA								FSTL5 (368352 upstream) : NAF1 (594321 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	163731567	163731567	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:163731567delA								FSTL5 (646381 upstream) : NAF1 (316293 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	164305128	164305128	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164305128delA								NPY5R (32044 upstream) : TKTL2 (87120 downstream)																																			---	---	---	---
MARCH1	55016	broad.mit.edu	37	4	164788407	164788407	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164788407delT	uc003iqs.1	-							NM_017923	NP_060393			membrane-associated RING-CH protein I						antigen processing and presentation of peptide antigen via MHC class II|immune response	cytoplasmic vesicle membrane|early endosome membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|plasma membrane	MHC protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)																---	---	---	---
MARCH1	55016	broad.mit.edu	37	4	165199298	165199299	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165199298_165199299insA	uc003iqs.1	-							NM_017923	NP_060393			membrane-associated RING-CH protein I						antigen processing and presentation of peptide antigen via MHC class II|immune response	cytoplasmic vesicle membrane|early endosome membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|plasma membrane	MHC protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	165747526	165747545	+	IGR	DEL	GAAGGAAGGAAGGAAGGAAG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165747526_165747545delGAAGGAAGGAAGGAAGGAAG								MARCH1 (442324 upstream) : TRIM61 (128055 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	165828408	165828409	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165828408_165828409delAC								MARCH1 (523206 upstream) : TRIM61 (47191 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	165865192	165865192	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165865192delA								MARCH1 (559990 upstream) : TRIM61 (10408 downstream)																																			---	---	---	---
DDX60	55601	broad.mit.edu	37	4	169193066	169193066	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169193066delA	uc003irp.2	-							NM_017631	NP_060101			DEAD (Asp-Glu-Ala-Asp) box polypeptide 60								ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0485)														---	---	---	---
PALLD	23022	broad.mit.edu	37	4	169589217	169589217	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169589217delT	uc011cjx.1	+						PALLD_uc003iru.2_Intron|PALLD_uc003irv.2_Intron	NM_016081	NP_057165			palladin isoform 2						cytoskeleton organization	actin filament|focal adhesion|lamellipodium|nucleus|ruffle|sarcomere	actin binding|muscle alpha-actinin binding			ovary(1)	1		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)										Pancreatic_Cancer_Familial_Clustering_of				---	---	---	---
CLCN3	1182	broad.mit.edu	37	4	170641253	170641253	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170641253delA	uc003isi.2	+	13					CLCN3_uc003ish.2_3'UTR|CLCN3_uc011cjz.1_3'UTR|CLCN3_uc011cka.1_3'UTR|uc003isk.1_5'Flank	NM_001829	NP_001820			chloride channel 3 isoform b						endosomal lumen acidification	cell surface|early endosome membrane|Golgi membrane|integral to membrane|late endosome membrane|transport vesicle membrane	antiporter activity|ATP binding|PDZ domain binding|protein heterodimerization activity|protein homodimerization activity|voltage-gated chloride channel activity			breast(2)|ovary(1)	3		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)														---	---	---	---
GLRA3	8001	broad.mit.edu	37	4	175598519	175598519	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175598519delT	uc003ity.1	-						GLRA3_uc003itz.1_Intron	NM_006529	NP_006520			glycine receptor, alpha 3 isoform a						synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|glycine binding|receptor activity|transmitter-gated ion channel activity			ovary(3)	3		Prostate(90;0.00601)|Breast(14;0.0091)|Melanoma(52;0.00959)|Renal(120;0.0183)|all_neural(102;0.0891)|all_hematologic(60;0.107)		all cancers(43;4.99e-18)|Epithelial(43;1.18e-16)|OV - Ovarian serous cystadenocarcinoma(60;5.88e-09)|STAD - Stomach adenocarcinoma(60;0.00442)|GBM - Glioblastoma multiforme(59;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0421)	Glycine(DB00145)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	182425481	182425481	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:182425481delT								None (None upstream) : MGC45800 (634678 downstream)																																			---	---	---	---
ODZ3	55714	broad.mit.edu	37	4	183491983	183491984	+	Intron	DEL	AA	-	-	rs35697079		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183491983_183491984delAA	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	183892078	183892078	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183892078delA								DCTD (53448 upstream) : FAM92A3 (66740 downstream)																																			---	---	---	---
WWC2	80014	broad.mit.edu	37	4	184159019	184159019	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184159019delT	uc010irx.2	+						WWC2_uc003ivk.3_Intron|WWC2_uc003ivl.3_Intron|WWC2_uc010iry.2_Intron|uc003ivm.2_Intron	NM_024949	NP_079225			WW and C2 domain containing 2											ovary(2)|lung(1)	3		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	184326509	184326510	+	IGR	INS	-	AA	AA	rs72422589		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184326509_184326510insAA								WWC2 (84582 upstream) : CDKN2AIP (39279 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	184423660	184423660	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184423660delT	uc003ivr.2	-						ING2_uc003ivs.1_5'Flank					Homo sapiens hypothetical gene supported by BC038563, mRNA (cDNA clone IMAGE:3917555).																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	187831005	187831005	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187831005delA								FAT1 (183155 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190563597	190563600	+	IGR	DEL	ACGC	-	-	rs66483179		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190563597_190563600delACGC								None (None upstream) : FRG1 (298374 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190582425	190582426	+	IGR	INS	-	G	G	rs71213139		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190582425_190582426insG								None (None upstream) : FRG1 (279548 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190614725	190614726	+	IGR	INS	-	AAA	AAA	rs68171076	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190614725_190614726insAAA								None (None upstream) : FRG1 (247248 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190619768	190619777	+	IGR	DEL	AAAACAAAAC	-	-	rs36202645		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190619768_190619777delAAAACAAAAC								None (None upstream) : FRG1 (242197 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190806529	190806530	+	Intron	DEL	AA	-	-	rs72720786		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190806529_190806530delAA	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	190844553	190844553	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190844553delA	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																														---	---	---	---
SLC9A3	6550	broad.mit.edu	37	5	482162	482162	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:482162delG	uc003jbe.2	-						SLC9A3_uc011clx.1_Intron	NM_004174	NP_004165			solute carrier family 9 (sodium/hydrogen							cell surface|integral to membrane	sodium:hydrogen antiporter activity				0			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)															---	---	---	---
CEP72	55722	broad.mit.edu	37	5	634238	634239	+	Intron	INS	-	A	A	rs147154043	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:634238_634239insA	uc003jbf.2	+						CEP72_uc011clz.1_Intron	NM_018140	NP_060610			centrosomal protein 72 kDa						G2/M transition of mitotic cell cycle|gamma-tubulin complex localization|spindle organization	centrosome|cytosol				ovary(1)	1			Epithelial(17;0.000339)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|Lung(60;0.0863)															---	---	---	---
TPPP	11076	broad.mit.edu	37	5	678128	678128	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:678128delG	uc003jbg.3	-	1	766	c.48delC	c.(46-48)CCCfs	p.P16fs	TPPP_uc003jbh.3_Frame_Shift_Del_p.P16fs	NM_007030	NP_008961	O94811	TPPP_HUMAN	tubulin polymerization promoting protein	16	Mediates interaction with LIMK1.				microtubule bundle formation|microtubule polymerization|positive regulation of protein polymerization	nucleus|perinuclear region of cytoplasm|soluble fraction	calcium ion binding|microtubule binding				0		Ovarian(839;0.0563)	Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)	GBM - Glioblastoma multiforme(108;0.0191)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	1906198	1906198	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1906198delC								IRX4 (23318 upstream) : IRX2 (840083 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	2286458	2286459	+	IGR	DEL	GT	-	-	rs145522495		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2286458_2286459delGT								IRX4 (403578 upstream) : IRX2 (459822 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	3459970	3459970	+	Intron	DEL	A	-	-	rs75518423		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3459970delA	uc003jdd.2	-											Homo sapiens cDNA clone IMAGE:4823480.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	4213464	4213464	+	IGR	DEL	T	-	-	rs11284959		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4213464delT								IRX1 (611948 upstream) : LOC340094 (821008 downstream)																																			---	---	---	---
LOC340094	340094	broad.mit.edu	37	5	5064678	5064678	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5064678delA	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	5410953	5410953	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5410953delA								ADAMTS16 (90542 upstream) : KIAA0947 (11854 downstream)																																			---	---	---	---
KIAA0947	23379	broad.mit.edu	37	5	5460422	5460422	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5460422delC	uc003jdm.3	+							NM_015325	NP_056140			hypothetical protein LOC23379											ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	5564776	5564777	+	IGR	INS	-	T	T	rs146028427	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5564776_5564777insT								KIAA0947 (74439 upstream) : FLJ33360 (745777 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	6156073	6156074	+	IGR	DEL	GA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6156073_6156074delGA								KIAA0947 (665736 upstream) : FLJ33360 (154480 downstream)																																			---	---	---	---
NSUN2	54888	broad.mit.edu	37	5	6617085	6617085	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6617085delA	uc003jdu.2	-						NSUN2_uc003jdt.2_Intron|NSUN2_uc011cmk.1_Intron|NSUN2_uc003jdv.2_Intron	NM_017755	NP_060225			NOL1/NOP2/Sun domain family, member 2							cytoplasm|nucleolus	tRNA (cytosine-5-)-methyltransferase activity|tRNA binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	7082066	7082066	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7082066delA								PAPD7 (324905 upstream) : ADCY2 (314277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	7920314	7920315	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7920314_7920315delTT								MTRR (19081 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	7958959	7958959	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7958959delG								MTRR (57726 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	8139844	8139860	+	IGR	DEL	TTCTTCACTTGTAAAAA	-	-	rs2308018		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8139844_8139860delTTCTTCACTTGTAAAAA								MTRR (238611 upstream) : SEMA5A (895278 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	8509584	8509584	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8509584delA								MTRR (608351 upstream) : SEMA5A (525554 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	9918296	9918297	+	IGR	DEL	GT	-	-	rs33937438		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9918296_9918297delGT								LOC285692 (14360 upstream) : FAM173B (308141 downstream)																																			---	---	---	---
MARCH6	10299	broad.mit.edu	37	5	10423317	10423318	+	Intron	INS	-	CTGA	CTGA	rs143508946	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10423317_10423318insCTGA	uc003jet.1	+						MARCH6_uc011cmu.1_Intron|MARCH6_uc003jeu.1_Intron|MARCH6_uc011cmv.1_Intron	NM_005885	NP_005876			membrane-associated ring finger (C3HC4) 6						protein K48-linked ubiquitination	integral to endoplasmic reticulum membrane	ubiquitin conjugating enzyme binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|breast(1)	2																		---	---	---	---
MARCH6	10299	broad.mit.edu	37	5	10424044	10424044	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10424044delT	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	10886142	10886142	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10886142delT								DAP (124755 upstream) : CTNND2 (85810 downstream)																																			---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	11241288	11241288	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11241288delA	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	12632640	12632640	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:12632640delT	uc003jfb.1	+						uc010itv.1_Intron					Homo sapiens TAG1 mRNA, complete sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	12900575	12900575	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:12900575delA								CTNND2 (996465 upstream) : DNAH5 (789862 downstream)																																			---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14186695	14186695	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14186695delT	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	14489275	14489275	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14489275delA	uc003jff.2	+						TRIO_uc003jfg.2_Intron	NM_007118	NP_009049			triple functional domain (PTPRF interacting)						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)																	---	---	---	---
ANKH	56172	broad.mit.edu	37	5	14856559	14856560	+	Intron	INS	-	AGGTCA	AGGTCA	rs148489987	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14856559_14856560insAGGTCA	uc003jfm.3	-							NM_054027	NP_473368			progressive ankylosis protein						locomotory behavior|regulation of bone mineralization|skeletal system development	integral to plasma membrane|outer membrane	inorganic diphosphate transmembrane transporter activity|inorganic phosphate transmembrane transporter activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
ANKH	56172	broad.mit.edu	37	5	14870158	14870159	+	Intron	INS	-	GAA	GAA	rs150942593	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14870158_14870159insGAA	uc003jfm.3	-							NM_054027	NP_473368			progressive ankylosis protein						locomotory behavior|regulation of bone mineralization|skeletal system development	integral to plasma membrane|outer membrane	inorganic diphosphate transmembrane transporter activity|inorganic phosphate transmembrane transporter activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	15313266	15313266	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15313266delT								ANKH (441379 upstream) : FBXL7 (187039 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	15342590	15342597	+	IGR	DEL	TTTTTTTT	-	-	rs113190254		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15342590_15342597delTTTTTTTT								ANKH (470703 upstream) : FBXL7 (157708 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	15456357	15456359	+	IGR	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15456357_15456359delTTT								ANKH (584470 upstream) : FBXL7 (43946 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	15495626	15495628	+	IGR	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15495626_15495628delTTT								ANKH (623739 upstream) : FBXL7 (4677 downstream)																																			---	---	---	---
FBXL7	23194	broad.mit.edu	37	5	15844914	15844914	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15844914delA	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																		---	---	---	---
FAM134B	54463	broad.mit.edu	37	5	16512692	16512692	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16512692delT	uc003jfs.2	-							NM_001034850	NP_001030022			hypothetical protein LOC54463 isoform 1						sensory perception of pain	cis-Golgi network|endoplasmic reticulum|integral to membrane				ovary(2)|breast(1)	3																		---	---	---	---
FAM134B	54463	broad.mit.edu	37	5	16603637	16603637	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16603637delG	uc003jfs.2	-							NM_001034850	NP_001030022			hypothetical protein LOC54463 isoform 1						sensory perception of pain	cis-Golgi network|endoplasmic reticulum|integral to membrane				ovary(2)|breast(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	17010264	17010265	+	IGR	DEL	TT	-	-	rs75612003		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17010264_17010265delTT								MYO10 (73879 upstream) : LOC285696 (119872 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	17316854	17316854	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17316854delC								BASP1 (39919 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	17670209	17670210	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17670209_17670210delAA								BASP1 (393274 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	17737122	17737122	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17737122delA								BASP1 (460187 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	17853659	17853659	+	Intron	DEL	A	-	-	rs80192893		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17853659delA	uc003jgb.2	+											Homo sapiens cDNA clone IMAGE:5201079.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	18279706	18279706	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18279706delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	19147372	19147373	+	IGR	INS	-	AAC	AAC	rs138317681	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19147372_19147373insAAC								None (None upstream) : CDH18 (325784 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	19282681	19282682	+	IGR	DEL	CA	-	-	rs10531189		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19282681_19282682delCA								None (None upstream) : CDH18 (190475 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	19294846	19294846	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19294846delT								None (None upstream) : CDH18 (178311 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	20189293	20189293	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20189293delT								CDH18 (200986 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	20575478	20575478	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20575478delG								CDH18 (587171 upstream) : GUSBP1 (766464 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	20833912	20833912	+	Intron	DEL	C	-	-	rs66590894		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20833912delC	uc003jge.1	+											Homo sapiens cDNA FLJ36043 fis, clone TESTI2017582.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	21590690	21590691	+	IGR	INS	-	TTT	TTT	rs145791738	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21590690_21590691insTTT								GUSBP1 (1211 upstream) : CDH12 (160282 downstream)																																			---	---	---	---
CDH12	1010	broad.mit.edu	37	5	21995926	21995926	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21995926delA	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	22001832	22001832	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22001832delT	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)			---	---	---	---
Unknown	0	broad.mit.edu	37	5	23298416	23298416	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23298416delA								CDH12 (444685 upstream) : PRDM9 (209308 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	25627161	25627161	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25627161delT								CDH10 (982250 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	26596445	26596445	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:26596445delA								None (None upstream) : CDH9 (284264 downstream)																																			---	---	---	---
CDH9	1007	broad.mit.edu	37	5	26963302	26963302	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:26963302delT	uc003jgs.1	-						CDH9_uc010iug.2_Intron	NM_016279	NP_057363			cadherin 9, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|skin(2)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	27054168	27054169	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27054168_27054169delTT								CDH9 (15479 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	27187793	27187794	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27187793_27187794delAC								CDH9 (149104 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	28423429	28423430	+	IGR	DEL	TT	-	-	rs34732090		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28423429_28423430delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	29429420	29429420	+	IGR	DEL	A	-	-	rs76642133		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:29429420delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	30374925	30374926	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30374925_30374926delAA								None (None upstream) : CDH6 (818870 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	30439006	30439006	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30439006delC								None (None upstream) : CDH6 (754790 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	30775601	30775601	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30775601delA								None (None upstream) : CDH6 (418195 downstream)																																			---	---	---	---
CDH6	1004	broad.mit.edu	37	5	31283132	31283132	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31283132delA	uc003jhe.1	+						CDH6_uc003jhd.1_Intron	NM_004932	NP_004923			cadherin 6, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	cytoplasm|integral to membrane|nucleus|plasma membrane	calcium ion binding			ovary(4)|skin(2)|large_intestine(1)	7																		---	---	---	---
PDZD2	23037	broad.mit.edu	37	5	31892021	31892021	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31892021delT	uc003jhl.2	+						PDZD2_uc003jhm.2_Intron|PDZD2_uc011cnx.1_Intron	NM_178140	NP_835260			PDZ domain containing 2						cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9																		---	---	---	---
PDZD2	23037	broad.mit.edu	37	5	32104469	32104472	+	Intron	DEL	TTTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32104469_32104472delTTTT	uc003jhl.2	+						PDZD2_uc003jhm.2_Intron|PDZD2_uc003jhn.2_Intron|PDZD2_uc003jho.2_5'Flank	NM_178140	NP_835260			PDZ domain containing 2						cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9																		---	---	---	---
MTMR12	54545	broad.mit.edu	37	5	32236945	32236945	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32236945delA	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	32323540	32323540	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32323540delA								MTMR12 (10426 upstream) : ZFR (30916 downstream)																																			---	---	---	---
SUB1	10923	broad.mit.edu	37	5	32603433	32603433	+	3'UTR	DEL	T	-	-	rs67981220		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32603433delT	uc003jhs.2	+	5					SUB1_uc003jht.2_RNA	NM_006713	NP_006704			activated RNA polymerase II transcription						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleolus|transcription factor complex	protein binding|single-stranded DNA binding|transcription coactivator activity				0																		---	---	---	---
NPR3	4883	broad.mit.edu	37	5	32739290	32739290	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32739290delT	uc003jhv.2	+						NPR3_uc010iuo.2_Intron|NPR3_uc011cnz.1_Intron|NPR3_uc003jhu.2_Intron	NM_000908	NP_000899			natriuretic peptide receptor C/guanylate cyclase						osteoclast proliferation|positive regulation of urine volume|regulation of blood pressure|regulation of osteoblast proliferation|skeletal system development	integral to membrane	hormone binding|natriuretic peptide receptor activity			ovary(1)|central_nervous_system(1)	2					Nesiritide(DB04899)													---	---	---	---
NPR3	4883	broad.mit.edu	37	5	32786466	32786466	+	3'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32786466delT	uc003jhv.2	+	8					NPR3_uc011cnz.1_3'UTR|NPR3_uc003jhu.2_3'UTR|C5orf23_uc003jhw.1_5'Flank	NM_000908	NP_000899			natriuretic peptide receptor C/guanylate cyclase						osteoclast proliferation|positive regulation of urine volume|regulation of blood pressure|regulation of osteoblast proliferation|skeletal system development	integral to membrane	hormone binding|natriuretic peptide receptor activity			ovary(1)|central_nervous_system(1)	2					Nesiritide(DB04899)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	32795219	32795219	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32795219delT								C5orf23 (3400 upstream) : TARS (645583 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	33156037	33156038	+	IGR	INS	-	AC	AC	rs143584003	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33156037_33156038insAC								C5orf23 (364218 upstream) : TARS (284764 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	33303026	33303026	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33303026delA								C5orf23 (511207 upstream) : TARS (137776 downstream)																																			---	---	---	---
SLC45A2	51151	broad.mit.edu	37	5	33984982	33984983	+	5'Flank	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33984982_33984983delTC	uc003jid.2	-						SLC45A2_uc003jie.2_5'Flank|SLC45A2_uc003jif.3_5'Flank|SLC45A2_uc011coe.1_5'Flank	NM_016180	NP_057264			membrane-associated transporter protein isoform						melanin biosynthetic process|response to stimulus|transmembrane transport|visual perception	integral to membrane|melanosome membrane				ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	34193721	34193721	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34193721delT	uc011cog.1	-						uc011coh.1_5'Flank|uc011coi.1_5'Flank					DQ598168																														---	---	---	---
SKP2	6502	broad.mit.edu	37	5	36169057	36169057	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36169057delG	uc003jkc.1	+						SKP2_uc011cou.1_Intron|SKP2_uc003jkd.2_Intron	NM_005983	NP_005974			S-phase kinase-associated protein 2 isoform 1						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)															---	---	---	---
NIPBL	25836	broad.mit.edu	37	5	37030863	37030863	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37030863delT	uc003jkl.3	+						NIPBL_uc003jkk.3_Intron	NM_133433	NP_597677			delangin isoform A						brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding			ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	9	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)															---	---	---	---
C5orf42	65250	broad.mit.edu	37	5	37138022	37138025	+	Intron	DEL	TTTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37138022_37138025delTTTT	uc011cpa.1	-						C5orf42_uc003jkp.1_Intron|C5orf42_uc011coy.1_Intron|C5orf42_uc003jks.2_Intron|C5orf42_uc011coz.1_Intron	NM_023073	NP_075561			hypothetical protein LOC65250											ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)															---	---	---	---
C5orf42	65250	broad.mit.edu	37	5	37162787	37162787	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37162787delT	uc011cpa.1	-						C5orf42_uc011coy.1_Intron|C5orf42_uc003jks.2_Intron|C5orf42_uc011coz.1_Intron	NM_023073	NP_075561			hypothetical protein LOC65250											ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)															---	---	---	---
C5orf42	65250	broad.mit.edu	37	5	37169770	37169770	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37169770delA	uc011cpa.1	-						C5orf42_uc011coy.1_Intron|C5orf42_uc003jks.2_Intron|C5orf42_uc011coz.1_Intron|C5orf42_uc003jkr.1_Intron	NM_023073	NP_075561			hypothetical protein LOC65250											ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)															---	---	---	---
C5orf42	65250	broad.mit.edu	37	5	37221410	37221410	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37221410delA	uc011cpa.1	-							NM_023073	NP_075561			hypothetical protein LOC65250											ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)															---	---	---	---
WDR70	55100	broad.mit.edu	37	5	37412152	37412152	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37412152delA	uc003jkv.2	+						WDR70_uc010iva.1_Intron	NM_018034	NP_060504			WD repeat domain 70											ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	38190947	38190947	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38190947delA								GDNF (351165 upstream) : EGFLAM (67586 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	38602601	38602601	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38602601delT	uc003jlj.2	+											Homo sapiens cDNA clone IMAGE:4829282.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	38674396	38674396	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38674396delT								LIFR (78889 upstream) : OSMR (171732 downstream)																																			---	---	---	---
FYB	2533	broad.mit.edu	37	5	39119141	39119142	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39119141_39119142delAA	uc003jls.2	-						FYB_uc003jlt.2_Intron|FYB_uc003jlu.2_Intron|FYB_uc011cpl.1_Intron	NM_199335	NP_955367			FYN binding protein (FYB-120/130) isoform 2						cell junction assembly|immune response|intracellular protein kinase cascade|NLS-bearing substrate import into nucleus|protein phosphorylation|T cell receptor signaling pathway	cytosol|nucleus	protein binding			ovary(2)	2	all_lung(31;0.000343)		Epithelial(62;0.235)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	39795429	39795430	+	IGR	INS	-	TG	TG			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39795429_39795430insTG								DAB2 (370094 upstream) : PTGER4 (884602 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	40025219	40025220	+	IGR	INS	-	T	T	rs142234609	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40025219_40025220insT								DAB2 (599884 upstream) : PTGER4 (654812 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	40140487	40140488	+	IGR	INS	-	A	A	rs140438267	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40140487_40140488insA								DAB2 (715152 upstream) : PTGER4 (539544 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	40398547	40398547	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40398547delA								DAB2 (973212 upstream) : PTGER4 (281485 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	43069381	43069381	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43069381delT	uc010ivk.2	+											Homo sapiens cDNA, FLJ18440.																														---	---	---	---
HMGCS1	3157	broad.mit.edu	37	5	43290195	43290198	+	3'UTR	DEL	AAAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43290195_43290198delAAAA	uc003jnr.3	-	11					HMGCS1_uc003jnp.3_3'UTR|HMGCS1_uc003jnq.3_3'UTR	NM_001098272	NP_001091742			hydroxymethylglutaryl-CoA synthase 1						cholesterol biosynthetic process|isoprenoid biosynthetic process	cytosol|soluble fraction	hydroxymethylglutaryl-CoA synthase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	43364405	43364406	+	IGR	INS	-	TG	TG	rs145373904	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43364405_43364406insTG								HMGCS1 (50810 upstream) : CCL28 (12344 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	43370847	43370848	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43370847_43370848delTT								HMGCS1 (57252 upstream) : CCL28 (5902 downstream)																																			---	---	---	---
PAIP1	10605	broad.mit.edu	37	5	43535227	43535227	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43535227delA	uc003job.2	-						PAIP1_uc003joa.2_Intron|PAIP1_uc010ivp.2_Intron|PAIP1_uc010ivo.2_Intron|PAIP1_uc003joc.2_Intron	NM_006451	NP_006442			poly(A) binding protein interacting protein 1						mRNA stabilization|nuclear-transcribed mRNA poly(A) tail shortening|translational initiation	cytosol	protein binding|RNA binding|translation activator activity			ovary(1)	1	Lung NSC(6;2.07e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	5	43713717	43713717	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43713717delT								NNT (8050 upstream) : FGF10 (591380 downstream)																																			---	---	---	---
HCN1	348980	broad.mit.edu	37	5	45321730	45321730	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45321730delT	uc003jok.2	-							NM_021072	NP_066550			hyperpolarization activated cyclic							integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	45820331	45820332	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45820331_45820332insA								HCN1 (124111 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	49493307	49493308	+	IGR	INS	-	G	G	rs62386414		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:49493307_49493308insG								None (None upstream) : EMB (198725 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	49535214	49535214	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:49535214delA								None (None upstream) : EMB (156819 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	50275385	50275385	+	IGR	DEL	T	-	-	rs75978055		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:50275385delT								PARP8 (137216 upstream) : ISL1 (403573 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	50322358	50322358	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:50322358delT								PARP8 (184189 upstream) : ISL1 (356600 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	50760870	50760870	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:50760870delT								ISL1 (70313 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	51144825	51144826	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:51144825_51144826insA								ISL1 (454268 upstream) : ITGA1 (938948 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	51269712	51269712	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:51269712delT								ISL1 (579155 upstream) : ITGA1 (814062 downstream)																																			---	---	---	---
ITGA2	3673	broad.mit.edu	37	5	52329099	52329099	+	Intron	DEL	A	-	-	rs3836831		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52329099delA	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	52447190	52447190	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52447190delT								MOCS2 (41592 upstream) : FST (329405 downstream)																																			---	---	---	---
ARL15	54622	broad.mit.edu	37	5	53377903	53377903	+	Intron	DEL	A	-	-	rs75518992		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53377903delA	uc003jpg.1	-						ARL15_uc010ivs.1_Intron	NM_019087	NP_061960			ADP-ribosylation factor-like 15								GTP binding			ovary(1)	1		Lung NSC(810;0.000779)																---	---	---	---
Unknown	0	broad.mit.edu	37	5	54538477	54538477	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54538477delT								CCNO (8969 upstream) : DHX29 (13597 downstream)																																			---	---	---	---
IL31RA	133396	broad.mit.edu	37	5	55178713	55178713	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55178713delG	uc003jql.2	+						IL31RA_uc003jqk.2_Intron|IL31RA_uc011cqj.1_Intron|IL31RA_uc003jqm.2_Intron|IL31RA_uc003jqn.2_Intron|IL31RA_uc010iwa.1_Intron|IL31RA_uc003jqo.2_Intron	NM_139017	NP_620586			gp130-like monocyte receptor						anti-apoptosis|defense response|homeostatic process|JAK-STAT cascade|macrophage differentiation|MAPKKK cascade|monocyte differentiation|negative regulation of macrophage activation|positive regulation of cell proliferation|positive regulation of transcription, DNA-dependent|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|transmembrane receptor protein tyrosine kinase signaling pathway	integral to membrane|plasma membrane	cytokine receptor activity|protein kinase binding|transcription coactivator activity			ovary(1)	1		Lung NSC(810;6.93e-05)|Prostate(74;0.00741)|Breast(144;0.0544)|Ovarian(174;0.223)																---	---	---	---
Unknown	0	broad.mit.edu	37	5	55379697	55379697	+	IGR	DEL	T	-	-	rs112776591		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55379697delT								IL6ST (88934 upstream) : ANKRD55 (15811 downstream)																																			---	---	---	---
ANKRD55	79722	broad.mit.edu	37	5	55466398	55466399	+	Intron	DEL	AA	-	-	rs34684342		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55466398_55466399delAA	uc003jqu.2	-							NM_024669	NP_078945			ankyrin repeat domain 55 isoform 1											skin(1)	1		Lung NSC(810;8.69e-05)|Prostate(74;0.00634)|Breast(144;0.0334)|Ovarian(174;0.223)																---	---	---	---
Unknown	0	broad.mit.edu	37	5	55912881	55912882	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55912881_55912882delAC								ANKRD55 (383695 upstream) : MAP3K1 (198018 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	56013390	56013390	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56013390delA								ANKRD55 (484204 upstream) : MAP3K1 (97510 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	56730774	56730774	+	IGR	DEL	T	-	-	rs75199036		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56730774delT								GPBP1 (171364 upstream) : ACTBL2 (45070 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	56973774	56973774	+	IGR	DEL	C	-	-	rs111449099		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56973774delC								ACTBL2 (195138 upstream) : PLK2 (776038 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	57458886	57458886	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57458886delT								ACTBL2 (680250 upstream) : PLK2 (290926 downstream)																																			---	---	---	---
PLK2	10769	broad.mit.edu	37	5	57754160	57754160	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57754160delA	uc003jrn.2	-						PLK2_uc011cql.1_Frame_Shift_Del_p.Y133fs	NM_006622	NP_006613			polo-like kinase 2						positive regulation of I-kappaB kinase/NF-kappaB cascade		ATP binding|protein binding|protein serine/threonine kinase activity|signal transducer activity			ovary(2)|lung(1)|skin(1)	4		all_cancers(5;1.76e-12)|all_epithelial(5;2.09e-13)|all_lung(5;6.64e-05)|Lung NSC(5;0.000127)|Prostate(74;0.055)|Breast(144;0.0602)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;7.03e-37)														---	---	---	---
PDE4D	5144	broad.mit.edu	37	5	58304127	58304127	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:58304127delA	uc003jsa.2	-						PDE4D_uc003jrx.2_Intron|PDE4D_uc003jry.2_Intron|PDE4D_uc003jrz.2_Intron|PDE4D_uc003jsb.2_Intron|PDE4D_uc003jrt.2_Intron|PDE4D_uc003jru.2_Intron|PDE4D_uc003jrv.2_Intron|PDE4D_uc003jrw.2_Intron|PDE4D_uc010iwi.1_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	58777739	58777739	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:58777739delA	uc003jsa.2	-						PDE4D_uc003jrx.2_Intron|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	59413653	59413654	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59413653_59413654delAC	uc003jsb.2	-						PDE4D_uc010iwj.1_Intron|PDE4D_uc003jse.1_Intron	NM_006203	NP_006194			phosphodiesterase 4D isoform 2						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)													---	---	---	---
PDE4D	5144	broad.mit.edu	37	5	59555787	59555787	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59555787delA	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)													---	---	---	---
PART1	25859	broad.mit.edu	37	5	59830704	59830704	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59830704delT	uc003jsg.2	+							NR_024617				Homo sapiens PART-1 mRNA, complete cds.												0																		---	---	---	---
FLJ37543	285668	broad.mit.edu	37	5	60987054	60987055	+	Intron	DEL	GA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60987054_60987055delGA	uc003jst.1	+						uc003jsv.2_Intron	NM_173667	NP_775938			hypothetical protein LOC285668 precursor							extracellular region					0		Lung NSC(810;0.000468)|Prostate(74;0.0283)|Breast(144;0.237)																---	---	---	---
Unknown	0	broad.mit.edu	37	5	61075481	61075482	+	IGR	INS	-	AG	AG			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61075481_61075482insAG								FLJ37543 (73119 upstream) : KIF2A (526507 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	61351723	61351723	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61351723delT								FLJ37543 (349361 upstream) : KIF2A (250266 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	61357200	61357200	+	IGR	DEL	T	-	-	rs35219963		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61357200delT								FLJ37543 (354838 upstream) : KIF2A (244789 downstream)																																			---	---	---	---
KIF2A	3796	broad.mit.edu	37	5	61635674	61635675	+	Intron	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61635674_61635675delTG	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	62239868	62239868	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:62239868delA								ISCA1P1 (166698 upstream) : None (None downstream)																																			---	---	---	---
RGS7BP	401190	broad.mit.edu	37	5	63809244	63809244	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63809244delT	uc003jtj.2	+							NM_001029875	NP_001025046			regulator of G-protein signaling 7 binding						negative regulation of signal transduction	cytoplasm|nucleus|plasma membrane					0		Lung NSC(810;0.000518)|Prostate(74;0.0435)|Ovarian(174;0.186)		Lung(70;0.147)														---	---	---	---
CENPK	64105	broad.mit.edu	37	5	64843498	64843499	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64843498_64843499insT	uc003jts.2	-						CENPK_uc003jtt.2_Intron|CENPK_uc003jtu.2_Intron	NM_022145	NP_071428			SoxLZ/Sox6 leucine zipper binding protein						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	condensed chromosome kinetochore|cytosol|nucleoplasm					0		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00466)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	65839578	65839578	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65839578delT								SFRS12 (362866 upstream) : MAST4 (52598 downstream)																																			---	---	---	---
MAST4	375449	broad.mit.edu	37	5	65914636	65914636	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65914636delT	uc003jur.3	+						MAST4_uc010iwz.2_Intron	NM_198828	NP_942123			microtubule associated serine/threonine kinase							cytoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	66589320	66589321	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66589320_66589321delTT								CD180 (96703 upstream) : PIK3R1 (922283 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	67294131	67294131	+	IGR	DEL	G	-	-	rs77900157		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67294131delG								CD180 (801514 upstream) : PIK3R1 (217473 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	67408330	67408330	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67408330delT								CD180 (915713 upstream) : PIK3R1 (103274 downstream)																																			---	---	---	---
PIK3R1	5295	broad.mit.edu	37	5	67583747	67583749	+	Intron	DEL	CTC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67583747_67583749delCTC	uc003jva.2	+						PIK3R1_uc003jvb.2_Intron|PIK3R1_uc003jvc.2_5'Flank|PIK3R1_uc003jvd.2_5'Flank|PIK3R1_uc003jve.2_5'Flank	NM_181523	NP_852664			phosphoinositide-3-kinase, regulatory subunit 1						epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex	1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding	p.?(1)		endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1)	101		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoproterenol(DB01064)			Mis|F|O		gliobastoma|ovarian|colorectal					TCGA GBM(4;<1E-08)			---	---	---	---
SLC30A5	64924	broad.mit.edu	37	5	68399960	68399960	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68399960delT	uc003jvh.2	+						SLC30A5_uc003jvg.2_3'UTR|SLC30A5_uc011crc.1_RNA|SLC30A5_uc003jvi.2_Intron	NM_022902	NP_075053			solute carrier family 30 (zinc transporter),						cellular zinc ion homeostasis|cobalt ion transport|regulation of proton transport|response to zinc ion	apical plasma membrane|Golgi apparatus|integral to plasma membrane|membrane fraction|secretory granule membrane	zinc ion binding|zinc ion transmembrane transporter activity			central_nervous_system(1)	1		Lung NSC(167;0.000986)|Prostate(74;0.00809)|Colorectal(97;0.0508)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)														---	---	---	---
GTF2H2B	653238	broad.mit.edu	37	5	69735940	69735943	+	Intron	DEL	AAAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:69735940_69735943delAAAA	uc003jzb.3	+						uc011crh.1_Intron|uc011crl.1_Intron|LOC100170939_uc010ixu.2_Intron|uc003jyr.1_Intron|LOC100170939_uc003jys.2_Intron|LOC100170939_uc011crn.1_Intron|uc011cro.1_Intron|GTF2H2B_uc011crp.1_Intron	NM_001098729	NP_001092199			general transcription factor IIH, polypeptide												0																		---	---	---	---
SMN2	6607	broad.mit.edu	37	5	70247737	70247737	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70247737delT	uc003kak.2	+						uc010iyh.1_Intron|uc003jzx.2_Intron|SMN1_uc011crr.1_Intron|SMN2_uc003kal.2_Intron|SMN2_uc003kam.2_Intron|SMN2_uc003kan.2_Intron|SMN2_uc003kap.1_Intron	NM_017411	NP_059107			survival of motor neuron 2, centromeric isoform						cell death|ncRNA metabolic process|spliceosomal snRNP assembly|spliceosome assembly	Cajal body|cytosol|spliceosomal complex	protein binding|protein binding|RNA binding				0		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)														---	---	---	---
MCCC2	64087	broad.mit.edu	37	5	70918097	70918098	+	Intron	INS	-	A	A	rs143752279	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70918097_70918098insA	uc003kbs.3	+						MCCC2_uc010iyv.1_Intron|MCCC2_uc003kbt.3_Intron|MCCC2_uc003kbu.1_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	71459383	71459383	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71459383delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	72001376	72001376	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72001376delT								ZNF366 (198127 upstream) : TNPO1 (111042 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	72018266	72018266	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72018266delA								ZNF366 (215017 upstream) : TNPO1 (94152 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	72542103	72542104	+	IGR	DEL	GC	-	-	rs142143272		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72542103_72542104delGC								TMEM174 (71135 upstream) : FOXD1 (199983 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	73791153	73791153	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73791153delA								RGNEF (553740 upstream) : ENC1 (132082 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	73878717	73878718	+	IGR	DEL	AA	-	-	rs77903446		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73878717_73878718delAA								RGNEF (641304 upstream) : ENC1 (44517 downstream)																																			---	---	---	---
FAM169A	26049	broad.mit.edu	37	5	74135799	74135799	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74135799delA	uc003kdm.2	-						FAM169A_uc010izm.2_Intron|FAM169A_uc003kdl.2_Intron	NM_015566	NP_056381			hypothetical protein LOC26049												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	74228865	74228865	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74228865delT								FAM169A (37077 upstream) : GCNT4 (94425 downstream)																																			---	---	---	---
HMGCR	3156	broad.mit.edu	37	5	74650644	74650644	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74650644delT	uc003kdp.2	+						HMGCR_uc011cst.1_Intron|HMGCR_uc003kdq.2_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)													---	---	---	---
IQGAP2	10788	broad.mit.edu	37	5	75960694	75960694	+	Intron	DEL	A	-	-	rs79165446		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75960694delA	uc003kek.2	+						IQGAP2_uc010izv.2_Intron|IQGAP2_uc011csv.1_Intron|IQGAP2_uc003kel.2_Intron	NM_006633	NP_006624			IQ motif containing GTPase activating protein 2						small GTPase mediated signal transduction	actin cytoskeleton	actin binding|calmodulin binding|GTPase inhibitor activity|Ras GTPase activator activity			ovary(6)|central_nervous_system(1)	7		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)														---	---	---	---
S100Z	170591	broad.mit.edu	37	5	76174029	76174029	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76174029delA	uc003kep.1	+	4					S100Z_uc003keq.3_Intron	NM_130772	NP_570128			S100 calcium binding protein Z								calcium ion binding			ovary(1)	1		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;8.91e-51)|Epithelial(54;5.43e-45)|all cancers(79;1.82e-40)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	76226930	76226931	+	IGR	DEL	TT	-	-	rs76291745		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76226930_76226931delTT								S100Z (9875 upstream) : CRHBP (21749 downstream)																																			---	---	---	---
CRHBP	1393	broad.mit.edu	37	5	76264841	76264842	+	3'UTR	DEL	CA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76264841_76264842delCA	uc003ker.2	+	7						NM_001882	NP_001873			corticotropin releasing hormone binding protein						female pregnancy|learning or memory|signal transduction	soluble fraction					0		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;2.17e-51)|Epithelial(54;8.79e-46)|all cancers(79;2.49e-41)														---	---	---	---
PDE8B	8622	broad.mit.edu	37	5	76550419	76550419	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76550419delT	uc003kfa.2	+						PDE8B_uc003kfb.2_Intron|PDE8B_uc003kfc.2_Intron|PDE8B_uc003kfd.2_Intron|PDE8B_uc003kfe.2_Intron	NM_003719	NP_003710			phosphodiesterase 8B isoform 1						cyclic nucleotide metabolic process|regulation of transcription, DNA-dependent	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|two-component response regulator activity				0		all_lung(232;0.00043)|Lung NSC(167;0.00114)|Ovarian(174;0.0107)|Prostate(461;0.0605)		OV - Ovarian serous cystadenocarcinoma(54;2.21e-49)|Epithelial(54;5.82e-43)|all cancers(79;4.06e-38)														---	---	---	---
AP3B1	8546	broad.mit.edu	37	5	77379973	77379973	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77379973delA	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	78211187	78211187	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78211187delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	78470344	78470345	+	IGR	INS	-	C	C	rs142685459	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78470344_78470345insC								BHMT (42232 upstream) : JMY (61609 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	78500210	78500211	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78500210_78500211delAA								BHMT (72098 upstream) : JMY (31743 downstream)																																			---	---	---	---
JMY	133746	broad.mit.edu	37	5	78584540	78584540	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78584540delT	uc003kfx.3	+						JMY_uc003kfw.1_Intron	NM_152405	NP_689618			junction-mediating and regulatory protein						'de novo' actin filament nucleation|actin polymerization-dependent cell motility|Arp2/3 complex-mediated actin nucleation|cell cycle arrest|DNA repair|induction of apoptosis|positive regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter	cell leading edge|cytoplasm|cytoskeleton|nucleus	actin binding|transcription coactivator activity				0		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;4.45e-45)|Epithelial(54;5.85e-40)|all cancers(79;2.89e-35)														---	---	---	---
CMYA5	202333	broad.mit.edu	37	5	79038584	79038585	+	Intron	DEL	AA	-	-	rs111610940	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79038584_79038585delAA	uc003kgc.2	+							NM_153610	NP_705838			cardiomyopathy associated 5							perinuclear region of cytoplasm				ovary(6)|pancreas(2)|lung(1)	9		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	79173109	79173110	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79173109_79173110delTG								CMYA5 (77061 upstream) : MTX3 (99431 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	79240785	79240785	+	IGR	DEL	A	-	-	rs72451657		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79240785delA								CMYA5 (144737 upstream) : MTX3 (31756 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	79248222	79248223	+	IGR	INS	-	CT	CT			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79248222_79248223insCT								CMYA5 (152174 upstream) : MTX3 (24318 downstream)																																			---	---	---	---
THBS4	7060	broad.mit.edu	37	5	79359601	79359601	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79359601delG	uc003kgh.2	+							NM_003248	NP_003239			thrombospondin 4 precursor						endothelial cell-cell adhesion|myoblast migration|negative regulation of angiogenesis|positive regulation of endothelial cell proliferation|positive regulation of neutrophil chemotaxis|positive regulation of peptidyl-tyrosine phosphorylation	basement membrane|extracellular space	calcium ion binding|heparin binding|integrin binding|structural molecule activity				0		Lung NSC(167;0.00328)|all_lung(232;0.00355)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-45)|Epithelial(54;1.77e-39)|all cancers(79;3.2e-34)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	79594873	79594873	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79594873delA								SERINC5 (43003 upstream) : LOC644936 (46 downstream)																																			---	---	---	---
FAM151B	167555	broad.mit.edu	37	5	79785220	79785220	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79785220delT	uc003kgv.1	+						FAM151B_uc010jal.1_Intron	NM_205548	NP_991111			hypothetical protein LOC167555												0		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;8.21e-47)|Epithelial(54;8.3e-42)|all cancers(79;1.97e-36)														---	---	---	---
MSH3	4437	broad.mit.edu	37	5	80005029	80005032	+	Intron	DEL	TGTG	-	-	rs74510033		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80005029_80005032delTGTG	uc003kgz.2	+							NM_002439	NP_002430			mutS homolog 3						maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments	MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding			lung(2)|ovary(1)|breast(1)	4		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)									MMR					---	---	---	---
MSH3	4437	broad.mit.edu	37	5	80156405	80156405	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80156405delT	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					---	---	---	---
CKMT2	1160	broad.mit.edu	37	5	80538123	80538123	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80538123delT	uc003khc.3	+						RNU5E_uc011cto.1_Intron|CKMT2_uc010jaq.2_Intron|CKMT2_uc003khd.3_Intron|uc003khe.1_Intron|uc003khf.1_Intron|uc003khg.1_Intron	NM_001825	NP_001816			sarcomeric mitochondrial creatine kinase						creatine metabolic process|muscle contraction	mitochondrial inner membrane	ATP binding|creatine kinase activity				0		Lung NSC(167;0.00475)|all_lung(232;0.00502)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;2.29e-44)|Epithelial(54;1.05e-38)|all cancers(79;4.15e-34)	Creatine(DB00148)													---	---	---	---
SSBP2	23635	broad.mit.edu	37	5	80924814	80924814	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80924814delT	uc003kho.2	-						SSBP2_uc003khn.2_Intron|SSBP2_uc003khp.2_Intron|SSBP2_uc011ctp.1_Intron|SSBP2_uc011ctq.1_Intron|SSBP2_uc011ctr.1_Intron	NM_012446	NP_036578			single-stranded DNA binding protein 2						regulation of transcription, DNA-dependent	cytoplasm|nucleus	single-stranded DNA binding		SSBP2/JAK2(4)	haematopoietic_and_lymphoid_tissue(4)|skin(1)	5		Lung NSC(167;0.00154)|all_lung(232;0.00179)|Ovarian(174;0.0338)		OV - Ovarian serous cystadenocarcinoma(54;1.07e-41)|Epithelial(54;2.79e-35)|all cancers(79;1.18e-29)														---	---	---	---
ATG10	83734	broad.mit.edu	37	5	81404713	81404713	+	Intron	DEL	A	-	-	rs35556500		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81404713delA	uc003khs.2	+						ATG10_uc003khq.2_Intron|ATG10_uc003khr.2_Intron|ATG10_uc010jas.2_Intron	NM_001131028	NP_001124500			APG10 autophagy 10-like						autophagy in response to ER overload|positive regulation of protein modification process|protein lipidation|protein modification by small protein conjugation|protein transport	cytoplasm	Atg12 ligase activity|protein binding				0		Lung NSC(167;0.0258)|all_lung(232;0.0294)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;9.94e-41)|Epithelial(54;6.3e-36)|all cancers(79;2.31e-30)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	82264880	82264880	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82264880delA								ATP6AP1L (650734 upstream) : TMEM167A (83787 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	82328222	82328223	+	IGR	DEL	TT	-	-	rs112630599		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82328222_82328223delTT								ATP6AP1L (714076 upstream) : TMEM167A (20444 downstream)																																			---	---	---	---
VCAN	1462	broad.mit.edu	37	5	82768021	82768021	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82768021delT	uc003kii.3	+						VCAN_uc003kij.3_Intron|VCAN_uc010jau.2_Intron|VCAN_uc003kik.3_Intron|VCAN_uc003kih.3_Intron	NM_004385	NP_004376			versican isoform 1 precursor						cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(7)|skin(6)|lung(2)|central_nervous_system(1)	16		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)														---	---	---	---
VCAN	1462	broad.mit.edu	37	5	82832816	82832816	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82832816delT	uc003kii.3	+						VCAN_uc003kij.3_Intron|VCAN_uc010jau.2_Intron|VCAN_uc003kik.3_Intron|VCAN_uc003kil.3_5'UTR	NM_004385	NP_004376			versican isoform 1 precursor						cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(7)|skin(6)|lung(2)|central_nervous_system(1)	16		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)														---	---	---	---
HAPLN1	1404	broad.mit.edu	37	5	82979819	82979819	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82979819delG	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	83860122	83860122	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:83860122delT								EDIL3 (179511 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	84158981	84158981	+	IGR	DEL	T	-	-	rs113714413		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:84158981delT								EDIL3 (478370 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	84159382	84159382	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:84159382delT								EDIL3 (478771 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	84922776	84922777	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:84922776_84922777insT								None (None upstream) : NBPF22P (655485 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	85114908	85114908	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:85114908delT								None (None upstream) : NBPF22P (463354 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	86414946	86414947	+	5'Flank	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86414946_86414947delAA	uc003kit.2	+											Homo sapiens cDNA clone IMAGE:5444809, **** WARNING: chimeric clone ****.																														---	---	---	---
RASA1	5921	broad.mit.edu	37	5	86644899	86644900	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86644899_86644900delAA	uc003kiw.2	+						RASA1_uc010jav.2_Intron|RASA1_uc003kix.2_Intron|RASA1_uc011ctv.1_Intron|RASA1_uc011ctw.1_Intron|RASA1_uc010jaw.2_Intron	NM_002890	NP_002881			RAS p21 protein activator 1 isoform 1						cytokinesis|embryo development|intracellular signal transduction|negative regulation of cell-matrix adhesion|negative regulation of neuron apoptosis|negative regulation of Ras protein signal transduction|positive regulation of anti-apoptosis|regulation of actin filament polymerization|regulation of cell shape|regulation of RNA metabolic process|vasculogenesis	cytosol|intrinsic to internal side of plasma membrane	glycoprotein binding|GTPase binding|potassium channel inhibitor activity|Ras GTPase activator activity|receptor binding			upper_aerodigestive_tract(3)|ovary(1)|lung(1)	5		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)														---	---	---	---
CCNH	902	broad.mit.edu	37	5	86705006	86705007	+	Intron	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86705006_86705007delTC	uc003kjb.2	-						CCNH_uc003kiy.1_5'Flank|CCNH_uc003kiz.1_Intron|CCNH_uc003kja.2_Intron	NM_001239	NP_001230			cyclin H						G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mRNA capping|nucleotide-excision repair, DNA damage removal|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein phosphorylation|regulation of cyclin-dependent protein kinase activity|S phase of mitotic cell cycle|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	cyclin-dependent protein kinase activating kinase holoenzyme complex|holo TFIIH complex	protein kinase binding			ovary(2)|kidney(1)	3		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;9.01e-39)|Epithelial(54;5.08e-33)|all cancers(79;4.28e-28)									Direct_reversal_of_damage|NER					---	---	---	---
Unknown	0	broad.mit.edu	37	5	87123982	87123982	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87123982delT								CCNH (415146 upstream) : TMEM161B (367042 downstream)																																			---	---	---	---
TMEM161B	153396	broad.mit.edu	37	5	87524857	87524857	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87524857delA	uc003kjc.2	-						TMEM161B_uc011cty.1_Intron|TMEM161B_uc010jax.2_Intron|TMEM161B_uc011ctz.1_Intron	NM_153354	NP_699185			transmembrane protein 161B							integral to membrane				skin(2)	2		all_cancers(142;0.000275)|Lung NSC(167;0.00901)|all_lung(232;0.0111)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;6.24e-36)|Epithelial(54;6.8e-31)|all cancers(79;1.07e-26)														---	---	---	---
TMEM161B	153396	broad.mit.edu	37	5	87566328	87566328	+	5'Flank	DEL	G	-	-	rs115190496		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87566328delG	uc003kjc.2	-						TMEM161B_uc011cty.1_5'Flank|TMEM161B_uc010jax.2_5'Flank|TMEM161B_uc011ctz.1_5'Flank|uc003kjd.2_Intron|uc003kje.2_Intron	NM_153354	NP_699185			transmembrane protein 161B							integral to membrane				skin(2)	2		all_cancers(142;0.000275)|Lung NSC(167;0.00901)|all_lung(232;0.0111)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;6.24e-36)|Epithelial(54;6.8e-31)|all cancers(79;1.07e-26)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	88668547	88668547	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88668547delT								MEF2C (468678 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	89741258	89741258	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89741258delT								CETN3 (35655 upstream) : MBLAC2 (12764 downstream)																																			---	---	---	---
GPR98	84059	broad.mit.edu	37	5	89913133	89913134	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89913133_89913134delTT	uc003kju.2	+						GPR98_uc003kjt.2_Intron	NM_032119	NP_115495			G protein-coupled receptor 98 precursor						cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)														---	---	---	---
GPR98	84059	broad.mit.edu	37	5	90021500	90021500	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90021500delT	uc003kju.2	+						GPR98_uc003kjt.2_Intron|GPR98_uc003kjv.2_Intron	NM_032119	NP_115495			G protein-coupled receptor 98 precursor						cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)														---	---	---	---
ARRDC3	57561	broad.mit.edu	37	5	90674409	90674409	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90674409delT	uc003kjz.2	-						LOC100129716_uc003kka.3_5'Flank	NM_020801	NP_065852			arrestin domain containing 3						signal transduction	cytoplasm	protein binding			ovary(1)|breast(1)	2		all_cancers(142;2.22e-05)|all_epithelial(76;1.58e-07)|all_lung(232;0.000521)|Lung NSC(167;0.000548)|Ovarian(174;0.0798)|Colorectal(57;0.207)		OV - Ovarian serous cystadenocarcinoma(54;4.56e-30)|Epithelial(54;7.55e-26)|all cancers(79;3.63e-22)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	91349135	91349135	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:91349135delT								LOC100129716 (632604 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	92055024	92055024	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92055024delT								None (None upstream) : FLJ42709 (690041 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	92113190	92113190	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92113190delA								None (None upstream) : FLJ42709 (631875 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	92561023	92561024	+	IGR	DEL	AA	-	-	rs138025968		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92561023_92561024delAA								None (None upstream) : FLJ42709 (184041 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	92611662	92611662	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92611662delT								None (None upstream) : FLJ42709 (133403 downstream)																																			---	---	---	---
FLJ42709	441094	broad.mit.edu	37	5	92769716	92769716	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92769716delT	uc003kkc.2	-						FLJ42709_uc003kkd.2_Intron|FLJ42709_uc011cud.1_Intron|FLJ42709_uc003kke.2_Intron|FLJ42709_uc011cue.1_Intron|FLJ42709_uc010jbb.1_Intron|FLJ42709_uc003kkf.2_Intron|FLJ42709_uc003kkg.2_Intron					Homo sapiens cDNA FLJ38400 fis, clone FEBRA2008159.												0																		---	---	---	---
FLJ42709	441094	broad.mit.edu	37	5	92879248	92879248	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92879248delA	uc003kkc.2	-						FLJ42709_uc003kkd.2_Intron|FLJ42709_uc011cud.1_Intron|FLJ42709_uc003kke.2_Intron|FLJ42709_uc011cue.1_Intron|FLJ42709_uc010jbb.1_Intron|FLJ42709_uc003kkf.2_Intron|FLJ42709_uc003kkg.2_Intron|FLJ42709_uc010jbc.2_RNA|FLJ42709_uc003kki.2_RNA|FLJ42709_uc003kkh.2_RNA					Homo sapiens cDNA FLJ38400 fis, clone FEBRA2008159.												0																		---	---	---	---
FAM172A	83989	broad.mit.edu	37	5	93195126	93195126	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93195126delA	uc010jbd.2	-						FAM172A_uc011cuf.1_Intron|FAM172A_uc011cug.1_Intron|FAM172A_uc011cuh.1_Intron|FAM172A_uc011cui.1_Intron|FAM172A_uc011cuj.1_Intron	NM_032042	NP_114431			hypothetical protein LOC83989 isoform 1							endoplasmic reticulum|extracellular region					0																		---	---	---	---
MCTP1	79772	broad.mit.edu	37	5	94092591	94092591	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94092591delT	uc003kkx.2	-						MCTP1_uc003kkv.2_Intron|MCTP1_uc003kkw.2_Intron|MCTP1_uc003kku.2_Intron	NM_024717	NP_078993			multiple C2 domains, transmembrane 1 isoform L						calcium-mediated signaling	integral to membrane|membrane fraction	calcium ion binding			ovary(2)	2		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	94628645	94628645	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94628645delA								MCTP1 (8366 upstream) : FAM81B (98403 downstream)																																			---	---	---	---
FAM81B	153643	broad.mit.edu	37	5	94776556	94776556	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94776556delA	uc003kla.1	+						FAM81B_uc010jbe.1_Intron	NM_152548	NP_689761			hypothetical protein LOC153643											ovary(1)|skin(1)	2		all_cancers(142;1.1e-06)|all_epithelial(76;1.48e-09)|all_lung(232;0.000696)|Lung NSC(167;0.000947)|Ovarian(225;0.00473)		all cancers(79;1.04e-16)														---	---	---	---
TTC37	9652	broad.mit.edu	37	5	94807246	94807246	+	Intron	DEL	T	-	-	rs147754036		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94807246delT	uc003klb.2	-							NM_014639	NP_055454			tetratricopeptide repeat domain 37								binding			ovary(3)|pancreas(1)	4																		---	---	---	---
ARSK	153642	broad.mit.edu	37	5	94911068	94911068	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94911068delT	uc003kld.2	+						ARSK_uc010jbg.2_Intron|ARSK_uc011cum.1_Intron	NM_198150	NP_937793			arylsulfatase K precursor							extracellular region	arylsulfatase activity|metal ion binding			pancreas(1)	1		all_cancers(142;3.38e-06)|all_epithelial(76;6.57e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.00473)		all cancers(79;6.5e-16)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	95334760	95334760	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95334760delT								ELL2 (36985 upstream) : MIR583 (80082 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	95852848	95852848	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95852848delT								PCSK1 (83896 upstream) : CAST (144929 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	96386053	96386053	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96386053delA								LNPEP (20938 upstream) : LIX1 (41522 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	96839291	96839291	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96839291delC								RIOK2 (320286 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	97399858	97399859	+	IGR	INS	-	CAAATCT	CAAATCT	rs142026047	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:97399858_97399859insCAAATCT								RIOK2 (880853 upstream) : RGMB (705140 downstream)																																			---	---	---	---
CHD1	1105	broad.mit.edu	37	5	98208017	98208017	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98208017delT	uc003knf.2	-						CHD1_uc010jbn.2_5'UTR	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)													---	---	---	---
CHD1	1105	broad.mit.edu	37	5	98224946	98224946	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98224946delA	uc003knf.2	-							NM_001270	NP_001261			chromodomain helicase DNA binding protein 1						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding			lung(2)|ovary(1)|breast(1)|pancreas(1)	5		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	98682160	98682161	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98682160_98682161insA								CHD1 (419922 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	99059503	99059503	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:99059503delT								CHD1 (797265 upstream) : LOC100133050 (655706 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	99072493	99072496	+	IGR	DEL	GAGA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:99072493_99072496delGAGA								CHD1 (810255 upstream) : LOC100133050 (642713 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	99186274	99186274	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:99186274delA								CHD1 (924036 upstream) : LOC100133050 (528935 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	99863071	99863071	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:99863071delA	uc003kni.2	-											full-length cDNA clone CS0DJ013YK21 of T cells (Jurkat cell line) Cot 10-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	100417532	100417532	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:100417532delT								ST8SIA4 (178545 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	101182166	101182166	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:101182166delA								ST8SIA4 (943179 upstream) : SLCO4C1 (387528 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	101642924	101642926	+	IGR	DEL	AAG	-	-	rs5870024		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:101642924_101642926delAAG								SLCO4C1 (10671 upstream) : SLCO6A1 (64724 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	101974165	101974168	+	IGR	DEL	ACAC	-	-	rs113592272		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:101974165_101974168delACAC								SLCO6A1 (139445 upstream) : PAM (227359 downstream)																																			---	---	---	---
PAM	5066	broad.mit.edu	37	5	102352977	102352977	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102352977delT	uc003knw.2	+						PAM_uc003kns.2_Intron|PAM_uc003knt.2_Intron|PAM_uc003knu.2_Intron|PAM_uc003knv.2_Intron|PAM_uc011cuz.1_Intron|PAM_uc003knz.2_Intron	NM_000919	NP_000910			peptidylglycine alpha-amidating monooxygenase						peptide metabolic process|protein modification process	extracellular region|integral to membrane|stored secretory granule	L-ascorbic acid binding|peptidylamidoglycolate lyase activity|peptidylglycine monooxygenase activity|protein binding				0		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)													---	---	---	---
GIN1	54826	broad.mit.edu	37	5	102433548	102433548	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102433548delA	uc003koa.1	-						GIN1_uc003kob.1_Intron|GIN1_uc003koc.1_Intron	NM_017676	NP_060146			zinc finger, H2C2 domain containing						DNA integration		DNA binding			ovary(1)|skin(1)	2		all_cancers(142;3.23e-07)|all_epithelial(76;3.64e-10)|Prostate(80;0.00914)|Ovarian(225;0.0139)|Lung NSC(167;0.0212)|Colorectal(57;0.0249)|all_lung(232;0.0283)		Epithelial(69;3.57e-14)|COAD - Colon adenocarcinoma(37;0.00794)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	103308196	103308196	+	IGR	DEL	A	-	-	rs13176909	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:103308196delA								NUDT12 (409706 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	103446722	103446723	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:103446722_103446723insT								NUDT12 (548232 upstream) : RAB9BP1 (988452 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	104770748	104770749	+	IGR	DEL	TG	-	-	rs144105785		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:104770748_104770749delTG								RAB9BP1 (334950 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	105444744	105444745	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:105444744_105444745insT								None (None upstream) : None (None downstream)																																			---	---	---	---
FBXL17	64839	broad.mit.edu	37	5	107498192	107498192	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107498192delA	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)														---	---	---	---
FER	2241	broad.mit.edu	37	5	108191646	108191647	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108191646_108191647delTT	uc003kop.1	+						FER_uc011cve.1_Intron|FER_uc011cvf.1_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)														---	---	---	---
PJA2	9867	broad.mit.edu	37	5	108722349	108722349	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108722349delT	uc003kos.3	-							NM_014819	NP_055634			praja 2, RING-H2 motif containing						long-term memory|regulation of protein kinase A signaling cascade	cell junction|endoplasmic reticulum membrane|Golgi membrane|postsynaptic density|postsynaptic membrane	ligase activity|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|zinc ion binding			ovary(1)|skin(1)	2		all_cancers(142;4.4e-06)|all_epithelial(76;8.17e-08)|Prostate(80;0.00676)|Lung NSC(167;0.0436)|Ovarian(225;0.0443)|all_lung(232;0.053)|Colorectal(57;0.0946)|Breast(839;0.151)		OV - Ovarian serous cystadenocarcinoma(64;3.46e-10)|Epithelial(69;6.02e-09)|COAD - Colon adenocarcinoma(37;0.224)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	108997155	108997156	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108997155_108997156insA								PJA2 (251480 upstream) : MAN2A1 (28000 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	109404457	109404460	+	IGR	DEL	TGTT	-	-	rs149890921		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109404457_109404460delTGTT								MAN2A1 (201028 upstream) : TMEM232 (220474 downstream)																																			---	---	---	---
TMEM232	642987	broad.mit.edu	37	5	109843811	109843812	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109843811_109843812insA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	110977298	110977298	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110977298delA								STARD4 (129065 upstream) : C5orf13 (21025 downstream)																																			---	---	---	---
C5orf13	9315	broad.mit.edu	37	5	111187977	111187978	+	Intron	INS	-	T	T	rs139736524	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111187977_111187978insT	uc011cvr.1	-						C5orf13_uc011cvs.1_Intron	NM_001142475	NP_001135947			neuronal protein 3.1 isoform c							cytoplasm				skin(1)	1		all_cancers(142;0.00597)|all_epithelial(76;0.000144)|Prostate(80;0.0115)|Colorectal(10;0.0446)|Ovarian(225;0.156)		OV - Ovarian serous cystadenocarcinoma(64;5.45e-09)|Epithelial(69;2e-08)|all cancers(49;1.9e-06)|COAD - Colon adenocarcinoma(37;0.0514)|Colorectal(14;0.0629)														---	---	---	---
REEP5	7905	broad.mit.edu	37	5	112214308	112214309	+	3'UTR	DEL	TA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112214308_112214309delTA	uc003kqe.1	-	5					SRP19_uc011cvu.1_Intron|SRP19_uc011cvv.1_Intron|REEP5_uc011cvw.1_3'UTR|REEP5_uc011cvx.1_RNA|REEP5_uc011cvy.1_3'UTR|REEP5_uc011cvz.1_RNA	NM_005669	NP_005660			receptor accessory protein 5							integral to membrane	protein binding				0		all_cancers(142;4.41e-05)|all_epithelial(76;3.65e-07)|Colorectal(10;0.00115)|Prostate(80;0.00133)|Ovarian(225;0.0443)		Epithelial(69;1.3e-09)|OV - Ovarian serous cystadenocarcinoma(64;1.26e-08)|all cancers(49;3.56e-07)|Colorectal(14;0.00778)|COAD - Colon adenocarcinoma(37;0.013)														---	---	---	---
YTHDC2	64848	broad.mit.edu	37	5	112862206	112862206	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112862206delA	uc003kqn.2	+						YTHDC2_uc010jce.1_Intron|YTHDC2_uc010jcf.1_Intron	NM_022828	NP_073739			YTH domain containing 2								ATP binding|ATP-dependent helicase activity|nucleic acid binding			skin(2)|central_nervous_system(1)	3		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	112967976	112967976	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112967976delA								YTHDC2 (36997 upstream) : KCNN2 (730040 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	113688855	113688856	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:113688855_113688856insT								YTHDC2 (757876 upstream) : KCNN2 (9160 downstream)																																			---	---	---	---
KCNN2	3781	broad.mit.edu	37	5	113742031	113742032	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:113742031_113742032delTT	uc003kqo.2	+							NM_021614	NP_067627			small conductance calcium-activated potassium							integral to membrane	calmodulin binding|small conductance calcium-activated potassium channel activity			ovary(2)	2		all_cancers(142;2.86e-05)|all_epithelial(76;9.33e-06)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Breast(839;0.159)|Lung NSC(810;0.174)|all_lung(232;0.206)		OV - Ovarian serous cystadenocarcinoma(64;1.89e-08)|Epithelial(69;2.04e-08)|all cancers(49;3.74e-06)|COAD - Colon adenocarcinoma(37;0.142)|Colorectal(14;0.195)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	115729252	115729253	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115729252_115729253delTT								COMMD10 (100274 upstream) : SEMA6A (49999 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	115969173	115969174	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115969173_115969174insT								SEMA6A (58622 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	116550612	116550612	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116550612delT								SEMA6A (640061 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	116739946	116739946	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116739946delT								SEMA6A (829395 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	116895322	116895323	+	Intron	DEL	AT	-	-	rs187859	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116895322_116895323delAT	uc003kry.2	+											Homo sapiens cDNA clone IMAGE:5297581.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	117461053	117461053	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:117461053delA								None (None upstream) : DTWD2 (711518 downstream)																																			---	---	---	---
DTWD2	285605	broad.mit.edu	37	5	118296444	118296444	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118296444delA	uc003ksa.2	-							NM_173666	NP_775937			DTW domain containing 2												0		all_epithelial(76;0.0982)|Prostate(80;0.121)		OV - Ovarian serous cystadenocarcinoma(64;0.000228)|Epithelial(69;0.000941)|all cancers(49;0.00939)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	119056329	119056329	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119056329delA								FAM170A (84813 upstream) : PRR16 (743690 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	119276889	119276889	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119276889delC								FAM170A (305373 upstream) : PRR16 (523130 downstream)																																			---	---	---	---
SNCAIP	9627	broad.mit.edu	37	5	121737787	121737787	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121737787delA	uc003ksw.1	+						SNCAIP_uc011cwl.1_Intron|SNCAIP_uc010jct.2_Intron|SNCAIP_uc003ksx.1_Intron|SNCAIP_uc003ksy.1_Intron|SNCAIP_uc003ksz.1_Intron|SNCAIP_uc010jcu.2_Intron|SNCAIP_uc011cwm.1_Intron|SNCAIP_uc003kta.1_Intron|SNCAIP_uc010jcv.1_Intron|SNCAIP_uc010jcw.1_Intron|SNCAIP_uc010jcx.1_Intron	NM_005460	NP_005451			synuclein alpha interacting protein						cell death|dopamine metabolic process|regulation of inclusion body assembly|regulation of neurotransmitter secretion	cytoplasm|neuronal cell body|nucleolus|presynaptic membrane	ubiquitin protein ligase binding			ovary(1)|pancreas(1)	2		all_cancers(142;0.00787)|Prostate(80;0.0327)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	121863087	121863087	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121863087delT								SNCAIP (63293 upstream) : SNX2 (247663 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	122763061	122763061	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122763061delT								CEP120 (3809 upstream) : CSNK1G3 (84732 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	123424531	123424532	+	IGR	DEL	GA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123424531_123424532delGA								CSNK1G3 (472069 upstream) : ZNF608 (548078 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	123569154	123569157	+	IGR	DEL	AGGA	-	-	rs72496860		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123569154_123569157delAGGA								CSNK1G3 (616692 upstream) : ZNF608 (403453 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	124303939	124303940	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124303939_124303940delTT								ZNF608 (219439 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	124435593	124435593	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124435593delT								ZNF608 (351093 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	124610442	124610442	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124610442delT								ZNF608 (525942 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	125122509	125122510	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125122509_125122510delAC								None (None upstream) : GRAMD3 (573278 downstream)																																			---	---	---	---
GRAMD3	65983	broad.mit.edu	37	5	125819334	125819334	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125819334delA	uc003ktu.2	+						GRAMD3_uc011cwt.1_Intron|GRAMD3_uc011cwv.1_Intron|GRAMD3_uc011cww.1_Intron|GRAMD3_uc011cwx.1_Intron|GRAMD3_uc011cwy.1_Intron|GRAMD3_uc011cwz.1_Intron|GRAMD3_uc011cwu.1_Intron	NM_023927	NP_076416			GRAM domain containing 3 isoform 2											central_nervous_system(1)	1		Prostate(80;0.0928)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0401)|OV - Ovarian serous cystadenocarcinoma(64;0.0604)|all cancers(49;0.108)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	125834230	125834232	+	IGR	DEL	TTG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125834230_125834232delTTG								GRAMD3 (4379 upstream) : ALDH7A1 (44686 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	125874291	125874291	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125874291delA								GRAMD3 (44440 upstream) : ALDH7A1 (4627 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	126010778	126010779	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126010778_126010779delTT								C5orf48 (38804 upstream) : LMNB1 (102054 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	126099751	126099751	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126099751delA								C5orf48 (127777 upstream) : LMNB1 (13082 downstream)																																			---	---	---	---
FLJ44606	401207	broad.mit.edu	37	5	126400681	126400681	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126400681delT	uc003kug.1	-											Homo sapiens cDNA FLJ44606 fis, clone BRACE2005991.						electron transport chain|transport						0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	126430557	126430557	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126430557delT								FLJ44606 (21385 upstream) : MEGF10 (195899 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	126904508	126904508	+	IGR	DEL	A	-	-	rs71726823		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126904508delA								PRRC1 (13730 upstream) : CTXN3 (80205 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	127188782	127188782	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127188782delA								CTXN3 (194461 upstream) : FLJ33630 (87353 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	128075262	128075262	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128075262delA								FBN2 (201346 upstream) : SLC27A6 (225948 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	129119214	129119214	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129119214delA								ADAMTS19 (44838 upstream) : CHSY3 (121309 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	129614921	129614921	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129614921delA								CHSY3 (92595 upstream) : HINT1 (879954 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	129945029	129945029	+	IGR	DEL	A	-	-	rs147485891		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129945029delA								CHSY3 (422703 upstream) : HINT1 (549846 downstream)																																			---	---	---	---
CDC42SE2	56990	broad.mit.edu	37	5	130686953	130686953	+	Intron	DEL	T	-	-	rs76760709		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130686953delT	uc003kvh.2	+						CDC42SE2_uc003kvi.2_Intron|CDC42SE2_uc003kvj.2_Intron|CDC42SE2_uc003kvk.2_Intron|CDC42SE2_uc003kvl.2_Intron	NM_020240	NP_064625			CDC42 small effector 2						phagocytosis|regulation of cell shape|regulation of signal transduction	cell projection|cytoplasm|cytoskeleton|phagocytic cup	protein binding|structural molecule activity				0		all_cancers(142;0.0525)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
RAPGEF6	51735	broad.mit.edu	37	5	130857585	130857588	+	Intron	DEL	CTCT	-	-	rs71000993		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130857585_130857588delCTCT	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	131054951	131054951	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131054951delA	uc003kvp.1	-						FNIP1_uc003kvs.1_Intron|FNIP1_uc003kvt.1_Intron|FNIP1_uc010jdm.1_Intron|FNIP1_uc003kvu.2_Intron	NM_016340	NP_057424			PDZ domain-containing guanine nucleotide						Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding			ovary(1)|lung(1)|central_nervous_system(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	131513632	131513633	+	IGR	DEL	TT	-	-	rs113668408		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131513632_131513633delTT								CSF2 (101774 upstream) : P4HA2 (14673 downstream)																																			---	---	---	---
RAD50	10111	broad.mit.edu	37	5	131950524	131950524	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131950524delA	uc003kxi.2	+						RAD50_uc003kxh.2_Intron	NM_005732	NP_005723			RAD50 homolog isoform 1						DNA duplex unwinding|double-strand break repair via homologous recombination|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|telomere maintenance via telomerase	Mre11 complex|nuclear chromosome, telomeric region|nucleoplasm	ATP binding|DNA binding|nuclease activity|protein binding, bridging|zinc ion binding			lung(2)|ovary(1)|skin(1)	4		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)										Homologous_recombination					---	---	---	---
HSPA4	3308	broad.mit.edu	37	5	132415802	132415802	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132415802delT	uc003kyj.2	+							NM_002154	NP_002145			heat shock 70kDa protein 4						cellular chaperone-mediated protein complex assembly|protein import into mitochondrial outer membrane|response to unfolded protein	cytoplasm|nucleus	ATP binding			lung(1)|breast(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
FSTL4	23105	broad.mit.edu	37	5	132613005	132613005	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132613005delA	uc003kyn.1	-							NM_015082	NP_055897			follistatin-like 4 precursor							extracellular region	calcium ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
FSTL4	23105	broad.mit.edu	37	5	132878614	132878614	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132878614delT	uc003kyn.1	-							NM_015082	NP_055897			follistatin-like 4 precursor							extracellular region	calcium ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	133275143	133275143	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133275143delA								FSTL4 (326920 upstream) : C5orf15 (16056 downstream)																																			---	---	---	---
VDAC1	7416	broad.mit.edu	37	5	133310656	133310657	+	Intron	DEL	AC	-	-	rs71591211	byFrequency	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133310656_133310657delAC	uc003kyp.1	-						VDAC1_uc003kyq.1_Intron|VDAC1_uc003kyr.1_Intron	NM_003374	NP_003365			voltage-dependent anion channel 1						apoptosis|interspecies interaction between organisms	mitochondrial nucleoid|mitochondrial outer membrane|plasma membrane|pore complex	porin activity|protein binding|voltage-gated anion channel activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00806)|Kidney(363;0.02)		Dihydroxyaluminium(DB01375)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	135293751	135293751	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135293751delA								LECT2 (3028 upstream) : TGFBI (70833 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	135462968	135462968	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135462968delA								MIR886 (46671 upstream) : SMAD5OS (2237 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	136014869	136014869	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136014869delT								TRPC7 (321796 upstream) : SPOCK1 (296119 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	136042244	136042244	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136042244delA								TRPC7 (349171 upstream) : SPOCK1 (268744 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	136255161	136255161	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136255161delA								TRPC7 (562088 upstream) : SPOCK1 (55827 downstream)																																			---	---	---	---
SPOCK1	6695	broad.mit.edu	37	5	136374266	136374266	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136374266delA	uc003lbo.2	-						SPOCK1_uc003lbp.2_Intron	NM_004598	NP_004589			sparc/osteonectin, cwcv and kazal-like domains						cell adhesion|cell proliferation|cellular component movement|nervous system development|signal transduction	proteinaceous extracellular matrix	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
SPOCK1	6695	broad.mit.edu	37	5	136540967	136540968	+	Intron	INS	-	A	A	rs17721921	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136540967_136540968insA	uc003lbo.2	-						SPOCK1_uc003lbp.2_Intron	NM_004598	NP_004589			sparc/osteonectin, cwcv and kazal-like domains						cell adhesion|cell proliferation|cellular component movement|nervous system development|signal transduction	proteinaceous extracellular matrix	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	136930753	136930753	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136930753delA								SPOCK1 (95735 upstream) : KLHL3 (22437 downstream)																																			---	---	---	---
FAM13B	51306	broad.mit.edu	37	5	137321766	137321766	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137321766delT	uc003lbz.2	-						FAM13B_uc003lcb.2_Intron|FAM13B_uc003lca.2_Intron	NM_016603	NP_057687			hypothetical protein LOC51306 isoform 1						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0																		---	---	---	---
BRD8	10902	broad.mit.edu	37	5	137481088	137481089	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137481088_137481089insA	uc003lcf.1	-						BRD8_uc003lcc.1_Intron	NM_139199	NP_631938			bromodomain containing 8 isoform 2						cell surface receptor linked signaling pathway|histone H2A acetylation|histone H4 acetylation|regulation of growth|regulation of transcription from RNA polymerase II promoter	mitochondrion|NuA4 histone acetyltransferase complex	sequence-specific DNA binding transcription factor activity|thyroid hormone receptor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)															---	---	---	---
KDM3B	51780	broad.mit.edu	37	5	137715102	137715102	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137715102delT	uc003lcy.1	+						KDM3B_uc010jew.1_Intron	NM_016604	NP_057688			jumonji domain containing 1B						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			ovary(3)|upper_aerodigestive_tract(2)|lung(2)|kidney(2)|central_nervous_system(1)|skin(1)	11																		---	---	---	---
CTNNA1	1495	broad.mit.edu	37	5	138248773	138248773	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138248773delT	uc003ldh.2	+						CTNNA1_uc011cyx.1_Intron|CTNNA1_uc011cyy.1_Intron|CTNNA1_uc003ldi.2_Intron|CTNNA1_uc003ldj.2_Intron|CTNNA1_uc003ldl.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)															---	---	---	---
CTNNA1	1495	broad.mit.edu	37	5	138262418	138262418	+	Intron	DEL	A	-	-	rs66931166		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138262418delA	uc003ldh.2	+						CTNNA1_uc011cyx.1_Intron|CTNNA1_uc011cyy.1_Intron|CTNNA1_uc003ldi.2_Intron|CTNNA1_uc003ldj.2_Intron|CTNNA1_uc003ldl.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)															---	---	---	---
SIL1	64374	broad.mit.edu	37	5	138510327	138510327	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138510327delA	uc003ldo.2	-						SIL1_uc003ldn.2_Intron|SIL1_uc003ldp.2_Intron	NM_001037633	NP_001032722			SIL1 protein precursor						intracellular protein transport|protein folding|transmembrane transport	endoplasmic reticulum lumen	unfolded protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)											Marinesco-Sj_gren_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	5	138934476	138934476	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138934476delT								TMEM173 (72184 upstream) : UBE2D2 (6275 downstream)																																			---	---	---	---
PSD2	84249	broad.mit.edu	37	5	139172445	139172448	+	5'Flank	DEL	TTCC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139172445_139172448delTTCC	uc003leu.1	+							NM_032289	NP_115665			pleckstrin and Sec7 domain containing 2						regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	139432441	139432441	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139432441delA								NRG2 (9562 upstream) : PURA (61267 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	140009583	140009583	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140009583delT								SLC35A4 (60900 upstream) : CD14 (1734 downstream)																																			---	---	---	---
TMCO6	55374	broad.mit.edu	37	5	140017460	140017461	+	5'Flank	INS	-	GCTT	GCTT	rs150019028	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140017460_140017461insGCTT	uc003lgl.2	+						TMCO6_uc011czj.1_5'Flank|TMCO6_uc003lgm.2_5'Flank|TMCO6_uc010jft.2_5'Flank	NM_018502	NP_060972			transmembrane and coiled-coil domains 6						protein import into nucleus	cytoplasm|nuclear pore	binding|protein transporter activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
DIAPH1	1729	broad.mit.edu	37	5	140963624	140963625	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140963624_140963625delAA	uc003llb.3	-						DIAPH1_uc003llc.3_Intron	NM_005219	NP_005210			diaphanous 1 isoform 1						regulation of microtubule-based process|sensory perception of sound	cytoplasm|cytoskeleton|ruffle membrane	actin binding|receptor binding|Rho GTPase binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
GNPDA1	10007	broad.mit.edu	37	5	141381388	141381388	+	3'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141381388delT	uc003lmf.3	-	6					GNPDA1_uc003lmg.3_3'UTR|GNPDA1_uc010jgh.2_3'UTR|GNPDA1_uc003lmh.3_3'UTR	NM_005471	NP_005462			glucosamine-6-phosphate deaminase 1						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)															---	---	---	---
NDFIP1	80762	broad.mit.edu	37	5	141491948	141491948	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141491948delA	uc003lmi.3	+						NDFIP1_uc003lmj.1_Intron	NM_030571	NP_085048			Nedd4 family interacting protein 1						cellular iron ion homeostasis|negative regulation of gene expression|negative regulation of protein transport|negative regulation of transporter activity|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of protein ubiquitination	endosome membrane|extracellular region|Golgi membrane|integral to membrane|perinuclear region of cytoplasm	signal transducer activity				0		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	141917007	141917007	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141917007delA								SPRY4 (212387 upstream) : FGF1 (54737 downstream)																																			---	---	---	---
ARHGAP26	23092	broad.mit.edu	37	5	142350662	142350662	+	Intron	DEL	T	-	-	rs3756393	byFrequency;by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142350662delT	uc011dbj.1	+						ARHGAP26_uc003lmt.2_Intron|ARHGAP26_uc003lmw.2_Intron	NM_015071	NP_055886			GTPase regulator associated with the focal						actin cytoskeleton organization|filopodium assembly|nervous system development|small GTPase mediated signal transduction	cytoskeleton|cytosol|focal adhesion	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(1)	1		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	142627257	142627260	+	IGR	DEL	TGGA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142627257_142627260delTGGA								ARHGAP26 (18686 upstream) : NR3C1 (30237 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	142939415	142939416	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142939415_142939416delTT								NR3C1 (124338 upstream) : HMHB1 (252310 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	144642341	144642341	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:144642341delA								KCTD16 (785397 upstream) : PRELID2 (496241 downstream)																																			---	---	---	---
SH3RF2	153769	broad.mit.edu	37	5	145322033	145322033	+	Intron	DEL	A	-	-	rs141623432	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145322033delA	uc003lnt.2	+						SH3RF2_uc011dbl.1_Intron	NM_152550	NP_689763			SH3 domain containing ring finger 2								ligase activity|protein phosphatase 1 binding|zinc ion binding			ovary(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
SH3RF2	153769	broad.mit.edu	37	5	145374777	145374777	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145374777delA	uc003lnt.2	+						SH3RF2_uc011dbl.1_Intron	NM_152550	NP_689763			SH3 domain containing ring finger 2								ligase activity|protein phosphatase 1 binding|zinc ion binding			ovary(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
SH3RF2	153769	broad.mit.edu	37	5	145440055	145440055	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145440055delA	uc003lnt.2	+						SH3RF2_uc011dbl.1_Intron|SH3RF2_uc003lnu.2_Intron|SH3RF2_uc011dbn.1_Intron|SH3RF2_uc011dbo.1_Intron	NM_152550	NP_689763			SH3 domain containing ring finger 2								ligase activity|protein phosphatase 1 binding|zinc ion binding			ovary(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	145491759	145491759	+	IGR	DEL	T	-	-	rs75849663		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145491759delT								PLAC8L1 (7813 upstream) : LARS (830 downstream)																																			---	---	---	---
LARS	51520	broad.mit.edu	37	5	145508516	145508516	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145508516delA	uc003lnx.1	-						LARS_uc003lnw.1_Intron|LARS_uc011dbq.1_Intron|LARS_uc011dbr.1_Intron|LARS_uc011dbs.1_Intron	NM_020117	NP_064502			leucyl-tRNA synthetase						leucyl-tRNA aminoacylation	cytosol	ATP binding|leucine-tRNA ligase activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)													---	---	---	---
RBM27	54439	broad.mit.edu	37	5	145605437	145605437	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145605437delT	uc003lnz.3	+						RBM27_uc003lny.2_Intron	NM_018989	NP_061862			RNA binding motif protein 27						mRNA processing	cytoplasm|nuclear speck	nucleotide binding|RNA binding|zinc ion binding			central_nervous_system(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	145715576	145715576	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145715576delA								RBM27 (46794 upstream) : POU4F3 (3011 downstream)																																			---	---	---	---
PPP2R2B	5521	broad.mit.edu	37	5	146014851	146014851	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146014851delT	uc003loe.2	-						PPP2R2B_uc010jgm.2_Intron|PPP2R2B_uc003log.3_Intron|PPP2R2B_uc003lof.3_Intron|PPP2R2B_uc003loi.3_Intron|PPP2R2B_uc003loh.3_Intron|PPP2R2B_uc003loj.3_Intron|PPP2R2B_uc003lok.3_Intron|PPP2R2B_uc011dbu.1_Intron|PPP2R2B_uc011dbv.1_Intron	NM_004576	NP_004567			beta isoform of regulatory subunit B55, protein						apoptosis|signal transduction	cytoskeleton|mitochondrial outer membrane|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)|prostate(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
PPP2R2B	5521	broad.mit.edu	37	5	146443157	146443158	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146443157_146443158insA	uc011dbv.1	-						PPP2R2B_uc003loj.3_Intron|PPP2R2B_uc003lok.3_Intron|PPP2R2B_uc011dbu.1_Intron	NM_181675	NP_858061			beta isoform of regulatory subunit B55, protein						apoptosis|signal transduction	cytoskeleton|mitochondrial outer membrane|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)|prostate(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
DPYSL3	1809	broad.mit.edu	37	5	146881373	146881373	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146881373delA	uc003loo.2	-							NM_001387	NP_001378			dihydropyrimidinase-like 3						axon guidance|pyrimidine base catabolic process|signal transduction	cytosol|growth cone	dihydropyrimidinase activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
JAKMIP2	9832	broad.mit.edu	37	5	147003388	147003388	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147003388delT	uc003loq.1	-						JAKMIP2_uc011dbx.1_Intron|JAKMIP2_uc003lor.1_Intron|uc003lop.1_Intron|JAKMIP2_uc010jgo.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)															---	---	---	---
SPINK6	404203	broad.mit.edu	37	5	147585430	147585430	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147585430delA	uc003lpa.2	+							NM_205841	NP_995313			serine protease inhibitor, Kazal type 6							extracellular region	serine-type endopeptidase inhibitor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
SPINK7	84651	broad.mit.edu	37	5	147695441	147695441	+	3'UTR	DEL	T	-	-	rs74351593		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147695441delT	uc003lpd.2	+	4					uc003lpb.1_Intron	NM_032566	NP_115955			serine peptidase inhibitor, Kazal type 7							extracellular region	protein binding|serine-type endopeptidase inhibitor activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
HTR4	3360	broad.mit.edu	37	5	147902626	147902626	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147902626delA	uc003lpn.2	-						HTR4_uc010jgu.1_Intron|HTR4_uc003lpi.1_Intron|HTR4_uc003lpj.1_Intron|HTR4_uc003lpk.2_Intron|HTR4_uc011dby.1_Intron|HTR4_uc003lpl.2_Intron|HTR4_uc003lpm.2_Intron|HTR4_uc010jgv.2_Intron|HTR4_uc003lpo.1_Intron	NM_000870	NP_000861			serotonin 5-HT4 receptor isoform b						G-protein signaling, coupled to cyclic nucleotide second messenger|positive regulation of cell proliferation	endosome|integral to plasma membrane|membrane fraction	serotonin receptor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Cisapride(DB00604)|Rizatriptan(DB00953)|Tegaserod(DB01079)|Zolmitriptan(DB00315)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	148449040	148449041	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148449040_148449041delAA								SH3TC2 (6303 upstream) : ABLIM3 (72013 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	148491265	148491266	+	IGR	INS	-	GAGAG	GAGAG	rs142143413	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148491265_148491266insGAGAG								SH3TC2 (48528 upstream) : ABLIM3 (29788 downstream)																																			---	---	---	---
DCTN4	51164	broad.mit.edu	37	5	150135319	150135319	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150135319delA	uc003lsv.2	-						DCTN4_uc003lsu.2_Intron|DCTN4_uc010jhi.2_Intron|DCTN4_uc010jhj.2_Intron|DCTN4_uc011dck.1_Intron	NM_016221	NP_057305			dynactin 4 (p62) isoform b							centrosome|nucleus	protein N-terminus binding			central_nervous_system(1)	1		Medulloblastoma(196;0.167)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	150377267	150377267	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150377267delA								LOC134466 (51121 upstream) : GPX3 (22732 downstream)																																			---	---	---	---
GM2A	2760	broad.mit.edu	37	5	150737837	150737837	+	Intron	DEL	T	-	-	rs78805271		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150737837delT	uc011dcs.1	+							NM_000405				GM2 ganglioside activator precursor							lysosome|nucleolus	sphingolipid activator protein activity				0		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
G3BP1	10146	broad.mit.edu	37	5	151148854	151148854	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151148854delT	uc003lun.2	+						G3BP1_uc010jhy.1_5'Flank|G3BP1_uc003lum.2_5'Flank|G3BP1_uc011dcu.1_5'Flank|G3BP1_uc010jhz.2_5'Flank	NM_005754	NP_005745			Ras-GTPase-activating protein SH3-domain-binding						Ras protein signal transduction|transport	cytosol|nucleus|plasma membrane	ATP binding|ATP-dependent DNA helicase activity|ATP-dependent RNA helicase activity|DNA binding|endonuclease activity|protein binding|RNA binding			skin(3)|ovary(1)	4		all_hematologic(541;0.0338)|Medulloblastoma(196;0.091)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)															---	---	---	---
G3BP1	10146	broad.mit.edu	37	5	151179246	151179246	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151179246delA	uc003lun.2	+						G3BP1_uc003lum.2_Intron|G3BP1_uc011dcu.1_Intron|G3BP1_uc010jhz.2_Intron|G3BP1_uc003luq.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)															---	---	---	---
G3BP1	10146	broad.mit.edu	37	5	151180020	151180020	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151180020delA	uc003lun.2	+						G3BP1_uc003lum.2_Intron|G3BP1_uc011dcu.1_Intron|G3BP1_uc010jhz.2_Intron|G3BP1_uc003luq.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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	152000920	152000920	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:152000920delC	uc003luw.1	-						uc003lux.1_Intron					Homo sapiens cDNA FLJ35529 fis, clone SPLEN2001912.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	152017754	152017754	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:152017754delA	uc003luw.1	-						uc003lux.1_Intron					Homo sapiens cDNA FLJ35529 fis, clone SPLEN2001912.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	152678089	152678089	+	IGR	DEL	T	-	-	rs112260775		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:152678089delT								NMUR2 (893249 upstream) : GRIA1 (191086 downstream)																																			---	---	---	---
MIR1303	100302284	broad.mit.edu	37	5	154065299	154065300	+	5'Flank	INS	-	G	G	rs142523787	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154065299_154065300insG	hsa-mir-1303|MI0006370	+																							0																		---	---	---	---
MRPL22	29093	broad.mit.edu	37	5	154335911	154335911	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154335911delT	uc003lvy.3	+						MRPL22_uc003lvz.3_Intron	NM_014180	NP_054899			mitochondrial ribosomal protein L22 isoform a						translation	large ribosomal subunit|mitochondrion	structural constituent of ribosome				0	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	156204745	156204746	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156204745_156204746delAA								SGCD (9949 upstream) : PPP1R2P3 (72803 downstream)																																			---	---	---	---
TIMD4	91937	broad.mit.edu	37	5	156381896	156381896	+	Intron	DEL	T	-	-	rs71922795		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156381896delT	uc003lwh.2	-						TIMD4_uc010jii.2_Intron	NM_138379	NP_612388			T-cell immunoglobulin and mucin domain							integral to membrane				ovary(2)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
HAVCR2	84868	broad.mit.edu	37	5	156523939	156523940	+	Intron	DEL	AC	-	-	rs145088214		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156523939_156523940delAC	uc003lwk.1	-							NM_032782	NP_116171			T cell immunoglobulin mucin 3 precursor							integral to membrane					0	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
ITK	3702	broad.mit.edu	37	5	156640739	156640739	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156640739delT	uc003lwo.1	+							NM_005546	NP_005537			IL2-inducible T-cell kinase						cellular defense response|intracellular signal transduction|T cell receptor signaling pathway	cytosol|plasma membrane	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(12)|ovary(8)|skin(4)|stomach(1)|central_nervous_system(1)	26	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.1)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)					T	SYK	peripheral T-cell lymphoma								---	---	---	---
SOX30	11063	broad.mit.edu	37	5	157068236	157068236	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157068236delA	uc003lxb.1	-						SOX30_uc003lxc.1_Intron|SOX30_uc011dds.1_Intron	NM_178424	NP_848511			SRY (sex determining region Y)-box 30 isoform a						regulation of transcription from RNA polymerase II promoter|regulation of transcription, DNA-dependent|response to corticosteroid stimulus|transcription, DNA-dependent	nucleus|nucleus	sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity			ovary(1)|central_nervous_system(1)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	157680211	157680212	+	IGR	DEL	TG	-	-	rs10539598		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157680211_157680212delTG								CLINT1 (394043 upstream) : EBF1 (442712 downstream)																																			---	---	---	---
RNF145	153830	broad.mit.edu	37	5	158634513	158634513	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158634513delA	uc003lxp.2	-						RNF145_uc011ddy.1_5'UTR|RNF145_uc003lxo.1_Intron|RNF145_uc011ddz.1_Intron|RNF145_uc010jiq.1_Intron|RNF145_uc011dea.1_Intron	NM_144726	NP_653327			ring finger protein 145							integral to membrane	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	159141853	159141858	+	IGR	DEL	ACACAC	-	-	rs35060890		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159141853_159141858delACACAC								LOC285627 (248569 upstream) : ADRA1B (201882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	159925360	159925360	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159925360delA								MIR146A (12903 upstream) : ATP10B (64767 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	160345472	160345473	+	IGR	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160345472_160345473delGT								ATP10B (66253 upstream) : LOC285629 (13315 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	160457282	160457282	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160457282delT								LOC285629 (91649 upstream) : GABRB2 (258154 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	161410639	161410639	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161410639delA								GABRA1 (83676 upstream) : GABRG2 (84009 downstream)																																			---	---	---	---
GABRG2	2566	broad.mit.edu	37	5	161545169	161545169	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161545169delA	uc003lyz.3	+						GABRG2_uc010jjc.2_Intron|GABRG2_uc003lyy.3_Intron|GABRG2_uc011dej.1_Intron	NM_000816	NP_000807			gamma-aminobutyric acid A receptor, gamma 2						gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity|protein binding			ovary(4)|skin(1)	5	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	161712756	161712757	+	IGR	INS	-	TTCCTTCTTTCCTTCC	TTCCTTCTTTCCTTCC	rs151171564	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161712756_161712757insTTCCTTCTTTCCTTCC								GABRG2 (130212 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	162225793	162225793	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162225793delT								GABRG2 (643249 upstream) : CCNG1 (638784 downstream)																																			---	---	---	---
MAT2B	27430	broad.mit.edu	37	5	162939331	162939331	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162939331delT	uc003lzk.2	+						MAT2B_uc003lzj.2_Intron|MAT2B_uc003lzl.1_Intron	NM_013283	NP_037415			methionine adenosyltransferase II, beta isoform						extracellular polysaccharide biosynthetic process|methylation|S-adenosylmethionine biosynthetic process|xenobiotic metabolic process	cytosol|methionine adenosyltransferase complex|nucleus	dTDP-4-dehydrorhamnose reductase activity|methionine adenosyltransferase regulator activity|protein binding			upper_aerodigestive_tract(1)	1	Renal(175;0.000281)	Medulloblastoma(196;0.0208)|all_neural(177;0.0765)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.027)|OV - Ovarian serous cystadenocarcinoma(192;0.0406)|Epithelial(171;0.0797)	L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	163453855	163453855	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:163453855delT								MAT2B (507522 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	164357290	164357290	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164357290delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	164550105	164550105	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164550105delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	164878947	164878948	+	IGR	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164878947_164878948delCT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	165253273	165253273	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165253273delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	166371591	166371592	+	IGR	INS	-	A	A	rs143289821	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166371591_166371592insA								None (None upstream) : ODZ2 (340251 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	166416081	166416081	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166416081delT								None (None upstream) : ODZ2 (295762 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	166667264	166667264	+	IGR	DEL	T	-	-	rs75364402		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166667264delT								None (None upstream) : ODZ2 (44579 downstream)																																			---	---	---	---
ODZ2	57451	broad.mit.edu	37	5	167379581	167379581	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167379581delT	uc010jjd.2	+						ODZ2_uc003lzq.2_Intron|ODZ2_uc003lzr.3_Intron	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)														---	---	---	---
ODZ2	57451	broad.mit.edu	37	5	167411665	167411665	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167411665delA	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)														---	---	---	---
RARS	5917	broad.mit.edu	37	5	167944769	167944769	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167944769delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	168903143	168903144	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168903143_168903144insT								SLIT3 (175010 upstream) : CCDC99 (107494 downstream)																																			---	---	---	---
KCNIP1	30820	broad.mit.edu	37	5	169892657	169892658	+	Intron	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169892657_169892658delAG	uc003map.2	+							NM_001034838	NP_001030010			Kv channel interacting protein 1 isoform 3						detection of calcium ion|signal transduction|synaptic transmission	plasma membrane	potassium channel activity|voltage-gated ion channel activity			skin(2)	2	Renal(175;0.000159)|Lung NSC(126;0.0191)|all_lung(126;0.0297)	Medulloblastoma(196;0.0109)|all_neural(177;0.0177)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
RANBP17	64901	broad.mit.edu	37	5	170412162	170412163	+	Intron	INS	-	AC	AC			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170412162_170412163insAC	uc003mba.2	+						RANBP17_uc003max.1_Intron|RANBP17_uc003may.1_Intron|RANBP17_uc003maz.1_Intron|RANBP17_uc010jjr.1_Intron	NM_022897	NP_075048			RAN binding protein 17						mRNA transport|protein import into nucleus|transmembrane transport	cytoplasm|nuclear pore	GTP binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)					T	TRD@	ALL								---	---	---	---
RANBP17	64901	broad.mit.edu	37	5	170534481	170534481	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170534481delT	uc003mba.2	+						RANBP17_uc003max.1_Intron|RANBP17_uc003may.1_Intron|RANBP17_uc003maz.1_Intron|RANBP17_uc010jjr.1_Intron	NM_022897	NP_075048			RAN binding protein 17						mRNA transport|protein import into nucleus|transmembrane transport	cytoplasm|nuclear pore	GTP binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)					T	TRD@	ALL								---	---	---	---
RANBP17	64901	broad.mit.edu	37	5	170668998	170668999	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170668998_170668999delTT	uc003mba.2	+						RANBP17_uc003mbb.2_Intron|RANBP17_uc003mbd.2_Intron|RANBP17_uc010jjs.2_Intron	NM_022897	NP_075048			RAN binding protein 17						mRNA transport|protein import into nucleus|transmembrane transport	cytoplasm|nuclear pore	GTP binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)					T	TRD@	ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	5	170967897	170967897	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170967897delA								FGF18 (83735 upstream) : FBXW11 (320659 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	171733024	171733025	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171733024_171733025delAA								UBTD2 (22229 upstream) : SH3PXD2B (27480 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	171749517	171749520	+	IGR	DEL	TTTC	-	-	rs72268473		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171749517_171749520delTTTC								UBTD2 (38722 upstream) : SH3PXD2B (10985 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	171897306	171897306	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171897306delT								SH3PXD2B (15779 upstream) : NEURL1B (170970 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	172045407	172045407	+	IGR	DEL	A	-	-	rs67615447		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172045407delA								SH3PXD2B (163880 upstream) : NEURL1B (22869 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	172216099	172216099	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172216099delA								DUSP1 (17896 upstream) : ERGIC1 (45124 downstream)																																			---	---	---	---
ERGIC1	57222	broad.mit.edu	37	5	172350308	172350310	+	Intron	DEL	GGA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172350308_172350310delGGA	uc003mbw.3	+						ERGIC1_uc003mby.3_Intron|ERGIC1_uc011dfa.1_Intron	NM_001031711	NP_001026881			endoplasmic reticulum-golgi intermediate						ER to Golgi vesicle-mediated transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane	protein binding			skin(2)|ovary(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00344)|all_lung(126;0.00594)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	173123116	173123116	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173123116delG								BOD1 (79450 upstream) : CPEB4 (192215 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	173194023	173194023	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173194023delA								BOD1 (150357 upstream) : CPEB4 (121308 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	173440303	173440303	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173440303delT								C5orf47 (7161 upstream) : HMP19 (32421 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	174050487	174050487	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174050487delC								HMP19 (514306 upstream) : MSX2 (101088 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	174280602	174280603	+	IGR	INS	-	G	G	rs142554515	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174280602_174280603insG								MSX2 (122701 upstream) : DRD1 (587073 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	174569316	174569316	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174569316delA								MSX2 (411415 upstream) : DRD1 (298360 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	174578925	174578926	+	IGR	INS	-	A	A	rs74710639		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174578925_174578926insA								MSX2 (421024 upstream) : DRD1 (288750 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	174584108	174584108	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174584108delA								MSX2 (426207 upstream) : DRD1 (283568 downstream)																																			---	---	---	---
SFXN1	94081	broad.mit.edu	37	5	174923778	174923778	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174923778delT	uc003mda.2	+						SFXN1_uc003mdb.1_Intron	NM_022754	NP_073591			sideroflexin 1						iron ion homeostasis	integral to membrane	cation transmembrane transporter activity|protein binding			ovary(1)	1	all_cancers(89;0.00922)|Renal(175;0.000269)|Lung NSC(126;0.00515)|all_lung(126;0.00873)	Medulloblastoma(196;0.0399)|all_neural(177;0.0663)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	175336756	175336756	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175336756delG								CPLX2 (25733 upstream) : THOC3 (49780 downstream)																																			---	---	---	---
C5orf25	375484	broad.mit.edu	37	5	175688751	175688751	+	Intron	DEL	A	-	-	rs147245998		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175688751delA	uc003mds.3	+						C5orf25_uc003mdt.3_Intron|C5orf25_uc003mdr.3_Intron|C5orf25_uc011dfk.1_Intron					RecName: Full=Uncharacterized protein C5orf25;												0	all_cancers(89;0.00381)|Renal(175;0.000269)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	Kidney(146;0.119)														---	---	---	---
CDHR2	54825	broad.mit.edu	37	5	175974568	175974569	+	5'Flank	INS	-	A	A	rs140801108	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175974568_175974569insA	uc003mem.1	+							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																		---	---	---	---
FGFR4	2264	broad.mit.edu	37	5	176520077	176520077	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176520077delG	uc003mfl.2	+						FGFR4_uc003mfm.2_Intron|FGFR4_uc011dfu.1_Intron|FGFR4_uc011dfw.1_3'UTR|FGFR4_uc003mfo.2_Intron	NM_002011	NP_002002			fibroblast growth factor receptor 4 isoform 1						insulin receptor signaling pathway|positive regulation of cell proliferation	integral to plasma membrane	ATP binding|fibroblast growth factor binding|fibroblast growth factor receptor activity			lung(11)|stomach(1)|central_nervous_system(1)|breast(1)|skin(1)|prostate(1)	16	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	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)		Palifermin(DB00039)										TSP Lung(9;0.080)			---	---	---	---
NSD1	64324	broad.mit.edu	37	5	176615846	176615846	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176615846delA	uc003mfr.3	+						NSD1_uc003mft.3_Intron|NSD1_uc003mfs.1_Intron|NSD1_uc011dfx.1_Intron|NSD1_uc003mfp.2_Intron	NM_022455	NP_071900			nuclear receptor binding SET domain protein 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)				T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			---	---	---	---
NSD1	64324	broad.mit.edu	37	5	176722543	176722543	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176722543delA	uc003mfr.3	+	23					NSD1_uc003mft.3_3'UTR|NSD1_uc011dfx.1_3'UTR	NM_022455	NP_071900			nuclear receptor binding SET domain protein 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)				T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			---	---	---	---
Unknown	0	broad.mit.edu	37	5	177044949	177044949	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177044949delT								B4GALT7 (7626 upstream) : LOC202181 (552 downstream)																																			---	---	---	---
COL23A1	91522	broad.mit.edu	37	5	177724781	177724781	+	Intron	DEL	A	-	-	rs33962826		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177724781delA	uc003mje.2	-							NM_173465	NP_775736			collagen, type XXIII, alpha 1							collagen|integral to membrane|plasma membrane	protein binding			central_nervous_system(1)|skin(1)	2	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)														---	---	---	---
COL23A1	91522	broad.mit.edu	37	5	177953142	177953142	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177953142delA	uc003mje.2	-							NM_173465	NP_775736			collagen, type XXIII, alpha 1							collagen|integral to membrane|plasma membrane	protein binding			central_nervous_system(1)|skin(1)	2	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)														---	---	---	---
AACSL	729522	broad.mit.edu	37	5	178211646	178211646	+	Intron	DEL	C	-	-	rs71587682		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178211646delC	uc011dgl.1	-						AACSL_uc003mjk.2_Intron					Homo sapiens acetoacetyl-CoA synthetase-like, mRNA (cDNA clone IMAGE:3945810), partial cds.												0																		---	---	---	---
AACSL	729522	broad.mit.edu	37	5	178243229	178243229	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178243229delA	uc011dgl.1	-						AACSL_uc003mjk.2_Intron					Homo sapiens acetoacetyl-CoA synthetase-like, mRNA (cDNA clone IMAGE:3945810), partial cds.												0																		---	---	---	---
ZNF879	345462	broad.mit.edu	37	5	178452918	178452920	+	Intron	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178452918_178452920delAAA	uc003mjt.3	+							NM_001136116	NP_001129588			zinc finger protein 879						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1																		---	---	---	---
MAPK9	5601	broad.mit.edu	37	5	179689017	179689017	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179689017delA	uc003mls.3	-						MAPK9_uc003mlt.3_Intron|MAPK9_uc010jlc.2_Intron|MAPK9_uc003mlv.3_Intron|MAPK9_uc011dgx.1_Intron	NM_002752	NP_002743			mitogen-activated protein kinase 9 isoform JNK2						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of gene expression|positive regulation of macrophage derived foam cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|JUN kinase activity|protein binding|protein binding			central_nervous_system(2)|upper_aerodigestive_tract(1)|large_intestine(1)	4	all_cancers(89;6.54e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	all_cancers(40;0.0236)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
CNOT6	57472	broad.mit.edu	37	5	179921024	179921024	+	5'Flank	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179921024delA	uc003mlx.2	+						CNOT6_uc010jld.2_5'Flank|CNOT6_uc010jle.2_5'Flank	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)														---	---	---	---
MGAT1	4245	broad.mit.edu	37	5	180236825	180236826	+	Intron	DEL	CA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180236825_180236826delCA	uc010jlh.2	-						MGAT1_uc003mmh.3_5'Flank|MGAT1_uc003mmi.3_Intron	NM_001114617	NP_001108089			mannosyl (alpha-1,3-)-glycoprotein						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(1)	1	all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00356)|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)															---	---	---	---
BTNL3	10917	broad.mit.edu	37	5	180424411	180424411	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180424411delA	uc003mmr.2	+	3	724	c.596delA	c.(595-597)GAAfs	p.E199fs		NM_197975	NP_932079	Q6UXE8	BTNL3_HUMAN	butyrophilin-like 3 precursor	199	Ig-like V-type.|Extracellular (Potential).				lipid metabolic process	integral to membrane					0	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.00336)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)|all_lung(500;0.248)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000272)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	236130	236131	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:236130_236131delTC								None (None upstream) : DUSP22 (55970 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	361250	361250	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:361250delC								DUSP22 (9897 upstream) : IRF4 (30502 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	706568	706568	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:706568delA								EXOC2 (13459 upstream) : LOC285768 (254674 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	919571	919571	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:919571delC								EXOC2 (226462 upstream) : LOC285768 (41671 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	1123217	1123217	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1123217delT								LOC285768 (21650 upstream) : FOXQ1 (189458 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	1294238	1294238	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1294238delA								LOC285768 (192671 upstream) : FOXQ1 (18437 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	1380872	1380872	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1380872delA								FOXQ1 (65880 upstream) : FOXF2 (9197 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	1465888	1465891	+	IGR	DEL	AAAT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1465888_1465891delAAAT								FOXF2 (70057 upstream) : FOXC1 (144790 downstream)																																			---	---	---	---
GMDS	2762	broad.mit.edu	37	6	2026363	2026363	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2026363delA	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	2135830	2135832	+	Intron	DEL	CAT	-	-	rs143726904		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2135830_2135832delCAT	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	2174780	2174780	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2174780delT	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	2336142	2336142	+	IGR	DEL	A	-	-	rs35741415		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2336142delA								GMDS (90296 upstream) : C6orf195 (286830 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	2432803	2432803	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2432803delA	uc003mtu.1	+											Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 1572223.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	2477351	2477351	+	Intron	DEL	A	-	-	rs34121714		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2477351delA	uc003mtu.1	+						uc003mtv.2_Intron					Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 1572223.																														---	---	---	---
SERPINB6	5269	broad.mit.edu	37	6	2954723	2954723	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2954723delA	uc003muk.2	-						SERPINB6_uc003mui.2_Intron|SERPINB6_uc003muj.2_Intron|SERPINB6_uc003mul.2_Intron|SERPINB6_uc003mum.2_Intron|SERPINB6_uc003mun.2_Intron|SERPINB6_uc003muo.2_Intron	NM_004568	NP_004559			serine (or cysteine) proteinase inhibitor, clade						regulation of proteolysis	centrosome|cytosol|protein complex	protease binding|serine-type endopeptidase inhibitor activity				0	Ovarian(93;0.0412)	all_hematologic(90;0.0895)			Drotrecogin alfa(DB00055)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	3162762	3162762	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3162762delT								TUBB2A (4979 upstream) : TUBB2B (61734 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	3186445	3186445	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3186445delA	uc003mve.2	-						uc003mvf.2_Intron					Homo sapiens, clone IMAGE:4998578, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	3470297	3470298	+	IGR	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3470297_3470298delAG								SLC22A23 (13504 upstream) : C6orf145 (252538 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	3606705	3606706	+	IGR	INS	-	ACACACACAT	ACACACACAT	rs72508000		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3606705_3606706insACACACACAT								SLC22A23 (149912 upstream) : C6orf145 (116130 downstream)																																			---	---	---	---
PRPF4B	8899	broad.mit.edu	37	6	4059124	4059124	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	4384751	4384751	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4384751delA								PECI (248920 upstream) : CDYL (321642 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	4533962	4533962	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4533962delA								PECI (398131 upstream) : CDYL (172431 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	4549420	4549423	+	IGR	DEL	AGGA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4549420_4549423delAGGA								PECI (413589 upstream) : CDYL (156970 downstream)																																			---	---	---	---
CDYL	9425	broad.mit.edu	37	6	4736934	4736934	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4736934delT	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)														---	---	---	---
CDYL	9425	broad.mit.edu	37	6	4829468	4829468	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4829468delT	uc003mwi.2	+						CDYL_uc003mwj.2_Intron|CDYL_uc003mwk.2_Intron	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)														---	---	---	---
CDYL	9425	broad.mit.edu	37	6	4869334	4869334	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4869334delT	uc003mwi.2	+						CDYL_uc003mwj.2_Intron|CDYL_uc003mwk.2_Intron|CDYL_uc011dhx.1_Intron	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)														---	---	---	---
F13A1	2162	broad.mit.edu	37	6	6314219	6314220	+	Intron	INS	-	T	T	rs10690734		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6314219_6314220insT	uc003mwv.2	-						F13A1_uc011dib.1_Intron	NM_000129	NP_000120			coagulation factor XIII A1 subunit precursor						peptide cross-linking|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|pancreas(1)|skin(1)	6	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	6728709	6728709	+	Intron	DEL	A	-	-	rs78580952		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6728709delA	uc003mxa.2	+											Homo sapiens, clone IMAGE:5189615, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	7073432	7073433	+	IGR	DEL	AC	-	-	rs575187	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7073432_7073433delAC								LY86 (418216 upstream) : RREB1 (34755 downstream)																																			---	---	---	---
RREB1	6239	broad.mit.edu	37	6	7189300	7189300	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7189300delT	uc003mxc.2	+						RREB1_uc010jnw.2_Intron|RREB1_uc003mxb.2_Intron|RREB1_uc010jnx.2_Intron|RREB1_uc003mxd.2_Intron	NM_001003698	NP_001003698			ras responsive element binding protein 1 isoform						multicellular organismal development|positive regulation of transcription, DNA-dependent|Ras protein signal transduction|transcription from RNA polymerase II promoter	cytoplasm|nuclear speck	DNA binding|zinc ion binding			ovary(4)|large_intestine(2)|pancreas(2)|skin(2)|breast(1)	11	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	7320667	7320667	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7320667delT								SSR1 (7126 upstream) : CAGE1 (6222 downstream)																																			---	---	---	---
DSP	1832	broad.mit.edu	37	6	7562607	7562609	+	Intron	DEL	TTT	-	-	rs147191716		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7562607_7562609delTTT	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)														---	---	---	---
TXNDC5	81567	broad.mit.edu	37	6	8064686	8064686	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8064686delT	uc003mxw.2	-						MUTED_uc003mxy.2_5'Flank|MUTED_uc010joc.2_5'Flank|MUTED_uc010job.2_5'Flank	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	8553834	8553835	+	Intron	INS	-	A	A	rs146016212	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8553834_8553835insA	uc003mye.2	+											Homo sapiens, clone IMAGE:5539086, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	9015130	9015131	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9015130_9015131insA								HULC (361053 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	9305640	9305640	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9305640delT								HULC (651563 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	9411704	9411704	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9411704delG								HULC (757627 upstream) : TFAP2A (985213 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	10304802	10304803	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10304802_10304803delTT								None (None upstream) : TFAP2A (92114 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	10331422	10331422	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10331422delA								None (None upstream) : TFAP2A (65495 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	10453789	10453790	+	IGR	INS	-	A	A	rs149671205	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10453789_10453790insA								C6orf218 (18734 upstream) : GCNT2 (38666 downstream)																																			---	---	---	---
MAK	4117	broad.mit.edu	37	6	10808301	10808301	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10808301delA	uc003mzl.2	-						SYCP2L_uc011dim.1_Intron|TMEM14B_uc010jos.1_Intron|MAK_uc010jot.2_Intron|MAK_uc010jou.2_Intron|MAK_uc003mzm.2_Intron|MAK_uc010jov.1_Intron	NM_005906	NP_005897			male germ cell-associated kinase						cell differentiation|multicellular organismal development|spermatogenesis		ATP binding|cyclin-dependent protein kinase activity			breast(2)|skin(1)	3	Breast(50;0.107)|Ovarian(93;0.107)	all_hematologic(90;0.117)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	11160080	11160080	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11160080delG								LOC221710 (21116 upstream) : NEDD9 (23451 downstream)																																			---	---	---	---
NEDD9	4739	broad.mit.edu	37	6	11260168	11260169	+	Intron	INS	-	ACACACACACACAC	ACACACACACACAC	rs139640152	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11260168_11260169insACACACACACACAC	uc010joz.2	-						NEDD9_uc003mzw.3_Intron	NM_001142393	NP_001135865			neural precursor cell expressed, developmentally						actin filament bundle assembly|cell adhesion|cell division|integrin-mediated signaling pathway|mitosis|regulation of growth	cell cortex|focal adhesion|Golgi apparatus|lamellipodium|nucleus	protein binding				0	Breast(50;0.0768)|Ovarian(93;0.152)	all_hematologic(90;0.135)	Epithelial(50;0.0647)|all cancers(50;0.179)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	11501667	11501667	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11501667delT	uc003mzz.1	+											Homo sapiens cDNA clone IMAGE:5269873.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	11655092	11655092	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11655092delT								TMEM170B (71336 upstream) : C6orf105 (58798 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	11862304	11862304	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11862304delA								C6orf105 (83024 upstream) : HIVEP1 (150420 downstream)																																			---	---	---	---
HIVEP1	3096	broad.mit.edu	37	6	12033556	12033557	+	Intron	DEL	TG	-	-	rs58465582		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12033556_12033557delTG	uc003nac.2	+							NM_002114	NP_002105			human immunodeficiency virus type I enhancer						transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	12181302	12181302	+	IGR	DEL	T	-	-	rs143671633	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12181302delT								HIVEP1 (16071 upstream) : EDN1 (109227 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	12284739	12284742	+	IGR	DEL	AAGG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12284739_12284742delAAGG								HIVEP1 (119508 upstream) : EDN1 (5787 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	12334633	12334634	+	IGR	DEL	CA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12334633_12334634delCA								EDN1 (37207 upstream) : PHACTR1 (382254 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	12435747	12435747	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12435747delT								EDN1 (138321 upstream) : PHACTR1 (281141 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	12641607	12641608	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12641607_12641608delAA								EDN1 (344181 upstream) : PHACTR1 (75280 downstream)																																			---	---	---	---
PHACTR1	221692	broad.mit.edu	37	6	12872680	12872681	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12872680_12872681delAC	uc010jpc.2	+						PHACTR1_uc011dir.1_Intron|PHACTR1_uc003nag.1_Intron|PHACTR1_uc003nah.1_Intron|PHACTR1_uc003nai.2_Intron	NM_030948	NP_112210			phosphatase and actin regulator 1							cell junction|cytoplasm|synapse	actin binding|protein phosphatase inhibitor activity				0	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)															---	---	---	---
PHACTR1	221692	broad.mit.edu	37	6	13207823	13207824	+	Intron	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13207823_13207824delTG	uc010jpc.2	+						PHACTR1_uc011dir.1_Intron|PHACTR1_uc003nag.1_Intron|PHACTR1_uc003nah.1_Intron	NM_030948	NP_112210			phosphatase and actin regulator 1							cell junction|cytoplasm|synapse	actin binding|protein phosphatase inhibitor activity				0	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)															---	---	---	---
TBC1D7	51256	broad.mit.edu	37	6	13312926	13312926	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13312926delA	uc003naj.2	-						TBC1D7_uc011dis.1_Intron|TBC1D7_uc003nan.2_Intron|TBC1D7_uc003nal.2_Intron|TBC1D7_uc003nam.2_Intron|TBC1D7_uc003nao.2_Intron|TBC1D7_uc010jpd.2_Intron|TBC1D7_uc003nap.2_Intron	NM_016495	NP_057579			TBC1 domain family, member 7 isoform a						positive regulation of protein ubiquitination	cytoplasmic membrane-bounded vesicle	protein binding|Rab GTPase activator activity			ovary(1)	1	Breast(50;0.0296)|Ovarian(93;0.0339)	all_hematologic(90;0.135)	Epithelial(50;0.0784)|BRCA - Breast invasive adenocarcinoma(129;0.13)|all cancers(50;0.21)															---	---	---	---
TBC1D7	51256	broad.mit.edu	37	6	13320955	13320957	+	Intron	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13320955_13320957delAAA	uc003naj.2	-						TBC1D7_uc011dis.1_Intron|TBC1D7_uc003nan.2_Intron|TBC1D7_uc003nal.2_Intron|TBC1D7_uc003nam.2_Intron|TBC1D7_uc003nao.2_Intron|TBC1D7_uc010jpd.2_Intron|TBC1D7_uc003nap.2_Intron|TBC1D7_uc003naq.2_In_Frame_Del_p.F161del	NM_016495	NP_057579			TBC1 domain family, member 7 isoform a						positive regulation of protein ubiquitination	cytoplasmic membrane-bounded vesicle	protein binding|Rab GTPase activator activity			ovary(1)	1	Breast(50;0.0296)|Ovarian(93;0.0339)	all_hematologic(90;0.135)	Epithelial(50;0.0784)|BRCA - Breast invasive adenocarcinoma(129;0.13)|all cancers(50;0.21)															---	---	---	---
RNF182	221687	broad.mit.edu	37	6	13926200	13926201	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13926200_13926201delTT	uc003nbe.2	+						RNF182_uc003nbf.2_Intron|RNF182_uc003nbg.2_Intron	NM_152737	NP_689950			ring finger protein 182							cytoplasm|integral to membrane|intracellular membrane-bounded organelle	protein binding|ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)	3	Breast(50;0.00405)|Ovarian(93;0.0964)	all_hematologic(90;0.135)	Epithelial(50;0.195)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	14094298	14094298	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14094298delA								RNF182 (114065 upstream) : CD83 (23567 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	14928825	14928826	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14928825_14928826delAA								CD83 (791679 upstream) : JARID2 (316908 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	15687246	15687246	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15687246delA								DTNBP1 (23975 upstream) : MYLIP (442071 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	15710434	15710437	+	IGR	DEL	CTTT	-	-	rs12191708		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15710434_15710437delCTTT								DTNBP1 (47163 upstream) : MYLIP (418880 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	15724531	15724531	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15724531delC								DTNBP1 (61260 upstream) : MYLIP (404786 downstream)																																			---	---	---	---
ATXN1	6310	broad.mit.edu	37	6	16427107	16427107	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16427107delA	uc003nbt.2	-						ATXN1_uc010jpi.2_Intron|ATXN1_uc010jpj.1_Intron	NM_000332	NP_000323			ataxin 1						cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing	cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm	identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association			skin(3)|central_nervous_system(1)	4	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	16952058	16952058	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16952058delT								ATXN1 (190337 upstream) : RBM24 (329751 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	17041656	17041656	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17041656delA								ATXN1 (279935 upstream) : RBM24 (240153 downstream)																																			---	---	---	---
CAP2	10486	broad.mit.edu	37	6	17461420	17461421	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17461420_17461421delAA	uc003ncb.2	+						CAP2_uc010jpk.1_Intron|CAP2_uc011dja.1_Intron|CAP2_uc011djb.1_Intron|CAP2_uc011djc.1_Intron|CAP2_uc011djd.1_Intron	NM_006366	NP_006357			adenylyl cyclase-associated protein 2						activation of adenylate cyclase activity|axon guidance|cytoskeleton organization|establishment or maintenance of cell polarity|signal transduction	plasma membrane	actin binding			ovary(1)	1	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)															---	---	---	---
KIF13A	63971	broad.mit.edu	37	6	17771637	17771638	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17771637_17771638insA	uc003ncg.3	-						KIF13A_uc003ncf.2_Intron|KIF13A_uc003nch.3_Intron|KIF13A_uc003nci.3_Intron|KIF13A_uc003nce.1_Intron	NM_022113	NP_071396			kinesin family member 13A isoform a						cargo loading into vesicle|cell cycle|cytokinesis|endosome to lysosome transport|Golgi to plasma membrane protein transport|melanosome organization|plus-end-directed vesicle transport along microtubule	centrosome|endosome membrane|microtubule|midbody|trans-Golgi network membrane	ATP binding|microtubule motor activity|protein binding			large_intestine(2)|ovary(2)	4	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)															---	---	---	---
KIF13A	63971	broad.mit.edu	37	6	17917255	17917255	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17917255delA	uc003ncg.3	-						KIF13A_uc003ncf.2_Intron|KIF13A_uc003nch.3_Intron|KIF13A_uc003nci.3_Intron	NM_022113	NP_071396			kinesin family member 13A isoform a						cargo loading into vesicle|cell cycle|cytokinesis|endosome to lysosome transport|Golgi to plasma membrane protein transport|melanosome organization|plus-end-directed vesicle transport along microtubule	centrosome|endosome membrane|microtubule|midbody|trans-Golgi network membrane	ATP binding|microtubule motor activity|protein binding			large_intestine(2)|ovary(2)	4	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	18373139	18373139	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18373139delA								DEK (108340 upstream) : RNF144B (14455 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	18991270	18991270	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18991270delT								MIR548A1 (419159 upstream) : ID4 (846347 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	19076768	19076769	+	Intron	INS	-	A	A	rs139322901	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19076768_19076769insA	uc003ncu.1	-											Homo sapiens cDNA FLJ40266 fis, clone TESTI2026461.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	19266100	19266101	+	IGR	INS	-	G	G	rs139771671	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19266100_19266101insG								MIR548A1 (693989 upstream) : ID4 (571516 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	19639167	19639167	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19639167delT								None (None upstream) : ID4 (198450 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	19895633	19895633	+	IGR	DEL	A	-	-	rs34737886		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19895633delA								ID4 (54719 upstream) : MBOAT1 (205302 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	20352687	20352688	+	IGR	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20352687_20352688delCT								MBOAT1 (140017 upstream) : E2F3 (49449 downstream)																																			---	---	---	---
CDKAL1	54901	broad.mit.edu	37	6	20607931	20607931	+	Intron	DEL	T	-	-	rs9460532		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20607931delT	uc003ndc.1	+						CDKAL1_uc003ndd.1_Intron|CDKAL1_uc003nde.1_Intron	NM_017774	NP_060244			CDK5 regulatory subunit associated protein						RNA modification	integral to membrane	4 iron, 4 sulfur cluster binding|metal ion binding|transferase activity			ovary(2)	2	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)															---	---	---	---
FLJ22536	401237	broad.mit.edu	37	6	21693698	21693698	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21693698delT	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	21746415	21746422	+	Intron	DEL	TTTTTTTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21746415_21746422delTTTTTTTT	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	21948454	21948457	+	Intron	DEL	ACAG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21948454_21948457delACAG	uc003ndj.2	+						FLJ22536_uc011djk.1_Intron|FLJ22536_uc003ndl.2_Intron|FLJ22536_uc011djj.1_Intron|FLJ22536_uc003ndk.1_Intron	NR_015410				Homo sapiens cDNA FLJ12803 fis, clone NT2RP2002172.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	22431633	22431633	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22431633delA								PRL (128551 upstream) : HDGFL1 (138045 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	23394300	23394307	+	IGR	DEL	AAGAAAGA	-	-	rs28865605		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23394300_23394307delAAGAAAGA								HDGFL1 (823551 upstream) : NRSN1 (732107 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	23518260	23518260	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23518260delA								HDGFL1 (947511 upstream) : NRSN1 (608154 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	23607620	23607621	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23607620_23607621delTT								None (None upstream) : NRSN1 (518793 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	23698970	23698970	+	IGR	DEL	C	-	-	rs7751108	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23698970delC								None (None upstream) : NRSN1 (427444 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	24007050	24007050	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24007050delT								None (None upstream) : NRSN1 (119364 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	25273346	25273346	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25273346delT								CMAH (106553 upstream) : LRRC16A (6302 downstream)																																			---	---	---	---
SCGN	10590	broad.mit.edu	37	6	25655893	25655894	+	Intron	INS	-	T	T	rs147978296	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25655893_25655894insT	uc003nfb.2	+						SCGN_uc010jpz.2_Intron	NM_006998	NP_008929			secretagogin precursor							extracellular region|transport vesicle membrane	calcium ion binding			ovary(2)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	25742110	25742110	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25742110delA								HIST1H2BA (14538 upstream) : SLC17A4 (12817 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	25901146	25901146	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25901146delA								SLC17A3 (26675 upstream) : SLC17A2 (11845 downstream)																																			---	---	---	---
HMGN4	10473	broad.mit.edu	37	6	26544481	26544481	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26544481delT	uc003nig.2	+							NM_006353	NP_006344			high mobility group nucleosomal binding domain							chromatin|nucleus	DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	27024568	27024568	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27024568delT								C6orf41 (32816 upstream) : HIST1H2BJ (68194 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	27885052	27885054	+	IGR	DEL	TTT	-	-	rs138450150		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27885052_27885054delTTT								OR2B2 (4955 upstream) : OR2B6 (39965 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	28210535	28210536	+	IGR	DEL	AC	-	-	rs68170691		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28210535_28210536delAC								ZNF193 (9275 upstream) : ZKSCAN4 (1954 downstream)																																			---	---	---	---
ZKSCAN3	80317	broad.mit.edu	37	6	28329508	28329509	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28329508_28329509insT	uc003nle.3	+						ZKSCAN3_uc010jrc.2_Intron|ZKSCAN3_uc003nlf.3_Intron	NM_024493	NP_077819			zinc finger with KRAB and SCAN domains 3						positive regulation of transcription, DNA-dependent|viral reproduction	nucleus	chromatin binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	30249025	30249025	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30249025delT								HLA-L (14297 upstream) : HCG18 (6149 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	30644142	30644142	+	IGR	DEL	C	-	-	rs73727455		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30644142delC								DHX16 (3312 upstream) : KIAA1949 (26 downstream)																																			---	---	---	---
GTF2H4	2968	broad.mit.edu	37	6	30874489	30874492	+	5'Flank	DEL	ATTT	-	-	rs11359484		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30874489_30874492delATTT	uc003nsa.1	+						GTF2H4_uc010jsf.2_5'Flank|GTF2H4_uc011dmv.1_5'Flank|GTF2H4_uc003nsb.1_5'Flank|GTF2H4_uc011dmw.1_5'Flank	NM_001517	NP_001508			general transcription factor IIH, polypeptide 4,						mRNA capping|nucleotide-excision repair, DNA damage removal|positive regulation of viral transcription|protein phosphorylation|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	holo TFIIH complex	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|breast(1)	3													NER					---	---	---	---
VARS2	57176	broad.mit.edu	37	6	30892377	30892377	+	Intron	DEL	G	-	-	rs115696940	byFrequency;by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30892377delG	uc003nsc.1	+						VARS2_uc011dmx.1_Intron|VARS2_uc011dmy.1_Intron|VARS2_uc011dmz.1_Intron|VARS2_uc011dna.1_Intron|VARS2_uc011dnb.1_Intron|VARS2_uc011dnc.1_Intron|VARS2_uc011dnd.1_Intron|VARS2_uc010jsg.1_Intron|VARS2_uc010jsh.1_Intron	NM_020442	NP_065175			valyl-tRNA synthetase 2, mitochondrial						valyl-tRNA aminoacylation	mitochondrion	ATP binding|valine-tRNA ligase activity			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
HLA-B	3106	broad.mit.edu	37	6	31253306	31253306	+	Intron	DEL	A	-	-	rs5875304		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31253306delA	uc003ntf.2	-						HLA-C_uc003ntb.2_Intron|HLA-C_uc003ntc.1_Intron|HLA-B_uc010jsm.1_Intron|HLA-B_uc011dnk.1_Intron					SubName: Full=MHC class I antigen;						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	31378225	31378226	+	Intron	INS	-	CCT	CCT			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31378225_31378226insCCT	uc003ntk.1	+						MICA_uc003rxz.1_Intron					RecName: Full=MHC class I polypeptide-related sequence A;          Short=MIC-A; Flags: Precursor;												0		Ovarian(999;0.0253)																---	---	---	---
CSNK2B	1460	broad.mit.edu	37	6	31640225	31640225	+	3'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31640225delT	uc003nvs.1	+	8					LY6G5B_uc003nvt.1_3'UTR	NM_001320	NP_001311			casein kinase 2, beta polypeptide						adiponectin-mediated signaling pathway|axon guidance|cellular protein complex assembly|negative regulation of cell proliferation|regulation of DNA binding|Wnt receptor signaling pathway	cytosol|nucleus|protein kinase CK2 complex	identical protein binding|protein domain specific binding|protein kinase regulator activity|receptor binding|transcription factor binding				0																		---	---	---	---
BAT5	7920	broad.mit.edu	37	6	31666029	31666029	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31666029delA	uc003nvy.1	-						BAT5_uc003nvx.1_Intron|BAT5_uc011dny.1_Intron|BAT5_uc003nvz.1_Intron|BAT5_uc011dnz.1_Intron|BAT5_uc010jtc.1_Intron|BAT5_uc011doa.1_Intron	NM_021160	NP_066983			HLA-B associated transcript 5							integral to membrane	hydrolase activity|protein binding				0																		---	---	---	---
LY6G6F	259215	broad.mit.edu	37	6	31683728	31683731	+	Intron	DEL	GTGT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31683728_31683731delGTGT	uc003nwb.1	+						BAT5_uc011dnz.1_5'Flank|LY6G6E_uc011dob.1_5'Flank|LY6G6E_uc003nwc.2_5'Flank|LY6G6E_uc003nwd.2_5'Flank|LY6G6E_uc003nwe.2_5'Flank|LY6G6D_uc003nwf.1_Intron|LY6G6D_uc003nwg.1_Intron	NM_001003693	NP_001003693			G6f protein precursor							integral to membrane|plasma membrane				breast(1)|central_nervous_system(1)	2																		---	---	---	---
NOTCH4	4855	broad.mit.edu	37	6	32183640	32183640	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32183640delT	uc003obb.2	-						NOTCH4_uc011dpu.1_Intron|NOTCH4_uc011dpv.1_Intron	NM_004557	NP_004548			notch4 preproprotein						cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|protein heterodimerization activity|receptor activity			lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1)	22																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	32211078	32211078	+	IGR	DEL	T	-	-	rs140222512		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32211078delT								NOTCH4 (19234 upstream) : C6orf10 (45225 downstream)																																			---	---	---	---
HLA-DMB	3109	broad.mit.edu	37	6	32910723	32910724	+	5'Flank	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32910723_32910724delTT	uc003ocl.1	-						HLA-DMB_uc003ocj.1_5'Flank|HLA-DMB_uc011dql.1_5'Flank	NM_002118	NP_002109			major histocompatibility complex, class II, DM						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0																		---	---	---	---
CUTA	51596	broad.mit.edu	37	6	33385527	33385527	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33385527delC	uc003oej.1	-						CUTA_uc003oek.1_5'UTR|CUTA_uc003oel.1_Intron|CUTA_uc003oem.1_5'UTR|CUTA_uc003oen.1_Intron|SYNGAP1_uc003oeo.1_5'Flank|SYNGAP1_uc011dri.1_5'Flank|SYNGAP1_uc010juy.2_5'Flank	NM_001014840	NP_001014840			cutA divalent cation tolerance homolog isoform						protein localization|response to metal ion	membrane	enzyme binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	35173431	35173433	+	Intron	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35173431_35173433delAAA	uc003oke.2	-											Homo sapiens mRNA sequence.																														---	---	---	---
DEF6	50619	broad.mit.edu	37	6	35282966	35282967	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35282966_35282967insT	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																		---	---	---	---
KCTD20	222658	broad.mit.edu	37	6	36442433	36442433	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36442433delT	uc003ome.2	+						KCTD20_uc011dtm.1_Intron|KCTD20_uc011dtn.1_Intron|KCTD20_uc010jwk.2_Intron|KCTD20_uc011dto.1_Intron	NM_173562	NP_775833			potassium channel tetramerisation domain							voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)	2																		---	---	---	---
STK38	11329	broad.mit.edu	37	6	36510847	36510847	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36510847delT	uc003omg.2	-						STK38_uc003omh.2_Intron|STK38_uc003omi.2_Intron	NM_007271	NP_009202			serine/threonine kinase 38						intracellular protein kinase cascade|negative regulation of MAP kinase activity	cytoplasm|MLL5-L complex	ATP binding|magnesium ion binding|mitogen-activated protein kinase kinase kinase binding|protein serine/threonine kinase activity			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	36904405	36904405	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36904405delA								C6orf89 (7667 upstream) : PI16 (17804 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	36959052	36959052	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36959052delG								MTCH1 (5103 upstream) : FGD2 (14371 downstream)																																			---	---	---	---
TMEM217	221468	broad.mit.edu	37	6	37185946	37185949	+	Intron	DEL	TTTT	-	-	rs67884824		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37185946_37185949delTTTT	uc003onl.2	-						TMEM217_uc010jwr.2_Intron|TMEM217_uc010jws.2_Intron|TMEM217_uc003onm.3_3'UTR	NM_145316	NP_660359			transmembrane protein 217 isoform 1							integral to membrane					0																		---	---	---	---
BTBD9	114781	broad.mit.edu	37	6	38267233	38267234	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38267233_38267234insT	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																		---	---	---	---
KIF6	221458	broad.mit.edu	37	6	39602474	39602474	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39602474delA	uc003oot.2	-						KIF6_uc010jxa.1_Intron|KIF6_uc011dua.1_Intron|KIF6_uc010jxb.1_Intron	NM_145027	NP_659464			kinesin family member 6						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein binding			breast(2)|central_nervous_system(1)	3																		---	---	---	---
LRFN2	57497	broad.mit.edu	37	6	40404735	40404736	+	Intron	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40404735_40404736delGT	uc003oph.1	-							NM_020737	NP_065788			leucine rich repeat and fibronectin type III							cell junction|integral to membrane|postsynaptic membrane				ovary(2)|skin(1)	3	Ovarian(28;0.0418)|Colorectal(47;0.196)																	---	---	---	---
TREML3	340206	broad.mit.edu	37	6	41185829	41185829	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41185829delT	uc003oqb.2	-							NR_027256				Homo sapiens TREM-like transcript 3 (TLT3) mRNA, partial cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	41191240	41191240	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41191240delC								TREML3 (5555 upstream) : TREML4 (4822 downstream)																																			---	---	---	---
TREM1	54210	broad.mit.edu	37	6	41251457	41251458	+	Intron	INS	-	AC	AC	rs78308642		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41251457_41251458insAC	uc003oqf.1	-						TREM1_uc003oqg.1_Intron	NM_018643	NP_061113			triggering receptor expressed on myeloid cells 1						blood coagulation|humoral immune response|intracellular signal transduction|leukocyte migration	extracellular region|integral to membrane|intracellular|plasma membrane	receptor activity			breast(1)	1	Ovarian(28;0.0327)|Colorectal(47;0.196)				Glutathione(DB00143)													---	---	---	---
MDFI	4188	broad.mit.edu	37	6	41620909	41620909	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41620909delG	uc003oqp.3	+						MDFI_uc003oqq.3_Intron|MDFI_uc010jxn.2_Intron	NM_005586	NP_005577			MyoD family inhibitor						cytoplasmic sequestering of transcription factor|dorsal/ventral axis specification|negative regulation of DNA binding|negative regulation of transcription from RNA polymerase II promoter|negative regulation of Wnt receptor signaling pathway	cytoplasm|nucleus					0	Ovarian(28;0.0327)|Colorectal(47;0.121)		Colorectal(64;0.0123)|COAD - Colon adenocarcinoma(64;0.0264)|KIRC - Kidney renal clear cell carcinoma(1;0.138)															---	---	---	---
TFEB	7942	broad.mit.edu	37	6	41695134	41695134	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41695134delA	uc003oqs.1	-						TFEB_uc003oqt.1_Intron|TFEB_uc003oqu.1_Intron|TFEB_uc003oqv.1_Intron|TFEB_uc010jxo.1_Intron|TFEB_uc003oqx.1_Intron|TFEB_uc003oqz.1_Intron|TFEB_uc010jxq.1_Intron	NM_007162	NP_009093			transcription factor EB						embryonic placenta development|humoral immune response|positive regulation of transcription from RNA polymerase II promoter	cytoplasm	sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(1)	1	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;7.61e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)					T	ALPHA	renal (childhood epithelioid)								---	---	---	---
Unknown	0	broad.mit.edu	37	6	42433350	42433350	+	IGR	DEL	T	-	-	rs76886178	byFrequency;by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42433350delT								TRERF1 (13485 upstream) : UBR2 (98708 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	42484791	42484791	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42484791delA								TRERF1 (64926 upstream) : UBR2 (47267 downstream)																																			---	---	---	---
UBR2	23304	broad.mit.edu	37	6	42538828	42538828	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42538828delT	uc011dur.1	+						UBR2_uc003osf.2_Intron	NM_015255	NP_056070			ubiquitin protein ligase E3 component n-recognin						cellular response to leucine|chromatin silencing|histone H2A ubiquitination|negative regulation of TOR signaling cascade	nucleus|plasma membrane	leucine binding|zinc ion binding			ovary(3)|pancreas(1)	4	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)															---	---	---	---
UBR2	23304	broad.mit.edu	37	6	42606586	42606586	+	Intron	DEL	A	-	-	rs75025165		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42606586delA	uc011dur.1	+						UBR2_uc011dus.1_Intron|UBR2_uc010jxv.1_Intron|UBR2_uc003osh.2_Intron	NM_015255	NP_056070			ubiquitin protein ligase E3 component n-recognin						cellular response to leucine|chromatin silencing|histone H2A ubiquitination|negative regulation of TOR signaling cascade	nucleus|plasma membrane	leucine binding|zinc ion binding			ovary(3)|pancreas(1)	4	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)															---	---	---	---
PPP2R5D	5528	broad.mit.edu	37	6	42961210	42961210	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42961210delA	uc003oth.2	+						MEA1_uc010jyc.1_Intron|PPP2R5D_uc003otg.2_Intron|PPP2R5D_uc010jyd.2_Intron|PPP2R5D_uc011dva.1_Intron|PPP2R5D_uc003oti.2_Intron	NM_006245	NP_006236			delta isoform of regulatory subunit B56, protein						nervous system development|signal transduction	cytoplasm|nucleus|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			breast(1)|central_nervous_system(1)	2			Colorectal(64;0.00237)|all cancers(41;0.00411)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0664)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)															---	---	---	---
ABCC10	89845	broad.mit.edu	37	6	43403271	43403271	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43403271delA	uc003ouy.1	+						ABCC10_uc003ouz.1_Intron|ABCC10_uc010jyo.1_5'Flank	NM_033450	NP_258261			ATP-binding cassette, sub-family C, member 10							integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(6)|central_nervous_system(1)	7	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)															---	---	---	---
XPO5	57510	broad.mit.edu	37	6	43528049	43528049	+	Intron	DEL	A	-	-	rs74544728		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43528049delA	uc003ovp.2	-							NM_020750	NP_065801			exportin 5						gene silencing by RNA	cytosol|nucleoplasm	protein binding|tRNA binding			skin(2)|breast(1)|kidney(1)	4	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	44176712	44176712	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44176712delT								CAPN11 (24573 upstream) : SLC29A1 (10530 downstream)																																			---	---	---	---
SUPT3H	8464	broad.mit.edu	37	6	44790564	44790564	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44790564delT	uc003oxn.1	-							NM_003599	NP_003590			suppressor of Ty 3 homolog isoform 1						histone deubiquitination|histone H3 acetylation|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	STAGA complex|transcription factor TFTC complex	DNA binding|transcription coactivator activity			ovary(2)|breast(1)	3																		---	---	---	---
RUNX2	860	broad.mit.edu	37	6	45456453	45456454	+	Intron	INS	-	A	A	rs147579004	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45456453_45456454insA	uc011dvx.1	+						RUNX2_uc011dvy.1_Intron|RUNX2_uc003oxt.2_Intron	NM_001024630	NP_001019801			runt-related transcription factor 2 isoform a						negative regulation of transcription, DNA-dependent|osteoblast differentiation|positive regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	45542646	45542646	+	IGR	DEL	A	-	-	rs73737480		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45542646delA								RUNX2 (23828 upstream) : CLIC5 (323544 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	45746383	45746384	+	IGR	DEL	GA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45746383_45746384delGA								RUNX2 (227565 upstream) : CLIC5 (119806 downstream)																																			---	---	---	---
CLIC5	53405	broad.mit.edu	37	6	45872482	45872482	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45872482delT	uc003oxv.3	-						CLIC5_uc003oxu.3_Intron	NM_001114086	NP_001107558			chloride intracellular channel 5 isoform a						female pregnancy	actin cytoskeleton|cell cortex|chloride channel complex|Golgi apparatus|Golgi apparatus|insoluble fraction|microtubule organizing center	protein binding|voltage-gated chloride channel activity			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	48438067	48438067	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:48438067delT								C6orf138 (359124 upstream) : MUT (960927 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	49617976	49617976	+	IGR	DEL	A	-	-	rs80138661		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49617976delA								RHAG (13389 upstream) : CRISP2 (42096 downstream)																																			---	---	---	---
CRISP3	10321	broad.mit.edu	37	6	49701364	49701364	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49701364delT	uc003ozs.2	-							NM_006061	NP_006052			cysteine-rich secretory protein 3 precursor						innate immune response	proteinaceous extracellular matrix|specific granule				skin(2)	2	Lung NSC(77;0.0161)		KIRC - Kidney renal clear cell carcinoma(2;0.106)|Kidney(12;0.156)															---	---	---	---
CRISP1	167	broad.mit.edu	37	6	49816026	49816026	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49816026delA	uc003ozw.2	-						CRISP1_uc003ozx.2_Intron	NM_001131	NP_001122			acidic epididymal glycoprotein-like 1 isoform 1						fusion of sperm to egg plasma membrane	extracellular space					0	Lung NSC(77;0.0358)																	---	---	---	---
DEFB114	245928	broad.mit.edu	37	6	49928266	49928267	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49928266_49928267insA	uc011dwp.1	-							NM_001037499	NP_001032588			beta-defensin 114 precursor						defense response to bacterium	extracellular region				ovary(1)	1	Lung NSC(77;0.042)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	50044797	50044798	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50044797_50044798delTT								DEFB112 (28433 upstream) : TFAP2D (636459 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	50434051	50434051	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50434051delA	uc003pae.1	+											full-length cDNA clone CS0DD007YH13 of Neuroblastoma Cot 50-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	50596484	50596484	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50596484delA								DEFB112 (580120 upstream) : TFAP2D (84773 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	50832370	50832370	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50832370delT								TFAP2B (17045 upstream) : PKHD1 (647775 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	51343967	51343967	+	IGR	DEL	A	-	-	rs77081503		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51343967delA								TFAP2B (528642 upstream) : PKHD1 (136178 downstream)																																			---	---	---	---
PKHD1	5314	broad.mit.edu	37	6	51935416	51935416	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51935416delA	uc003pah.1	-						PKHD1_uc003pai.2_Intron	NM_138694	NP_619639			fibrocystin isoform 1						cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)																	---	---	---	---
PKHD1	5314	broad.mit.edu	37	6	51946933	51946933	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51946933delA	uc003pah.1	-						PKHD1_uc003pai.2_Intron	NM_138694	NP_619639			fibrocystin isoform 1						cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)																	---	---	---	---
PKHD1	5314	broad.mit.edu	37	6	51948067	51948067	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51948067delA	uc003pah.1	-						PKHD1_uc003pai.2_Intron	NM_138694	NP_619639			fibrocystin isoform 1						cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)																	---	---	---	---
EFHC1	114327	broad.mit.edu	37	6	52288681	52288681	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52288681delT	uc003pap.3	+						EFHC1_uc011dwv.1_Intron|EFHC1_uc011dww.1_Intron	NM_018100	NP_060570			EF-hand domain (C-terminal) containing 1							axoneme|neuronal cell body	calcium ion binding|protein C-terminus binding			ovary(2)|skin(1)	3	Lung NSC(77;0.109)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	52984513	52984513	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52984513delT								FBXO9 (18845 upstream) : GCM1 (7249 downstream)																																			---	---	---	---
KLHL31	401265	broad.mit.edu	37	6	53519514	53519514	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53519514delT	uc003pcb.3	-	2	698	c.557delA	c.(556-558)AATfs	p.N186fs		NM_001003760	NP_001003760	Q9H511	KLH31_HUMAN	kelch repeat and BTB (POZ) domain containing 1	186	BACK.				regulation of transcription, DNA-dependent|transcription, DNA-dependent					ovary(1)	1	Lung NSC(77;0.0158)																	---	---	---	---
LRRC1	55227	broad.mit.edu	37	6	53769795	53769795	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53769795delT	uc003pcd.1	+							NM_018214	NP_060684			leucine rich repeat containing 1							cytoplasm|membrane				ovary(1)	1	Lung NSC(77;0.0147)			BRCA - Breast invasive adenocarcinoma(397;0.0745)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	53816061	53816061	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53816061delA	uc003pce.2	+											Homo sapiens cDNA FLJ32022 fis, clone NTONG1000161.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	54144665	54144665	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54144665delA								C6orf142 (13591 upstream) : TINAG (28538 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	54924458	54924459	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54924458_54924459insT								FAM83B (117641 upstream) : HCRTR2 (85043 downstream)																																			---	---	---	---
COL21A1	81578	broad.mit.edu	37	6	56017474	56017474	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56017474delT	uc003pcs.2	-						COL21A1_uc003pct.1_Intron|COL21A1_uc011dxi.1_Intron|COL21A1_uc003pcu.1_Intron	NM_030820	NP_110447			collagen, type XXI, alpha 1 precursor						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(2)	2	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)															---	---	---	---
COL21A1	81578	broad.mit.edu	37	6	56047463	56047463	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56047463delA	uc003pcs.2	-						COL21A1_uc003pct.1_Intron|COL21A1_uc011dxi.1_Intron|COL21A1_uc003pcu.1_Intron	NM_030820	NP_110447			collagen, type XXI, alpha 1 precursor						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(2)	2	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)															---	---	---	---
DST	667	broad.mit.edu	37	6	56358106	56358106	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56358106delA	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc003pcy.3_Intron|DST_uc003pda.3_5'Flank	NM_001144769	NP_001138241			dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)															---	---	---	---
DST	667	broad.mit.edu	37	6	56374060	56374061	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56374060_56374061insT	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc003pcy.3_Intron	NM_001144769	NP_001138241			dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)															---	---	---	---
DST	667	broad.mit.edu	37	6	56476127	56476127	+	Intron	DEL	A	-	-	rs34186947		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56476127delA	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc003pcy.3_Intron|DST_uc003pdb.2_Intron	NM_001144769	NP_001138241			dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)															---	---	---	---
DST	667	broad.mit.edu	37	6	56589768	56589769	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56589768_56589769delAC	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc011dxl.1_Intron	NM_001144769	NP_001138241			dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)															---	---	---	---
ZNF451	26036	broad.mit.edu	37	6	57014629	57014629	+	Intron	DEL	T	-	-	rs66838312		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57014629delT	uc003pdm.1	+						ZNF451_uc003pdl.2_Intron|ZNF451_uc003pdn.1_Intron|uc003pdq.1_Intron|ZNF451_uc003pdk.1_Intron	NM_001031623	NP_001026794			zinc finger protein 451 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)|pancreas(1)	2	Lung NSC(77;0.145)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)															---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57193447	57193447	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57193447delA	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	57250114	57250114	+	Intron	DEL	T	-	-	rs145906273		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57250114delT	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	57309965	57309965	+	Intron	DEL	A	-	-	rs5876568		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57309965delA	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	57367402	57367402	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57367402delT	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	57380824	57380825	+	Intron	INS	-	TT	TT	rs145567229		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57380824_57380825insTT	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	57396574	57396574	+	Intron	DEL	A	-	-	rs79549638	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57396574delA	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	57402022	57402023	+	Intron	INS	-	G	G	rs144916181		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57402022_57402023insG	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	57544037	57544040	+	IGR	DEL	AACA	-	-	rs111449102	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57544037_57544040delAACA								PRIM2 (30662 upstream) : GUSBL2 (702119 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57592374	57592374	+	IGR	DEL	A	-	-	rs66776760		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57592374delA								PRIM2 (78999 upstream) : GUSBL2 (653785 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57676084	57676084	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57676084delA								PRIM2 (162709 upstream) : GUSBL2 (570075 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57836821	57836822	+	IGR	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57836821_57836822delCT								PRIM2 (323446 upstream) : GUSBL2 (409337 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	61955709	61955710	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:61955709_61955710insT								None (None upstream) : KHDRBS2 (434155 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	62266572	62266573	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:62266572_62266573insA								None (None upstream) : KHDRBS2 (123292 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	63067374	63067374	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63067374delT								KHDRBS2 (71274 upstream) : LGSN (918483 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	63071113	63071113	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63071113delT								KHDRBS2 (75013 upstream) : LGSN (914744 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	63084655	63084655	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63084655delA								KHDRBS2 (88555 upstream) : LGSN (901202 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	63103399	63103399	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63103399delA								KHDRBS2 (107299 upstream) : LGSN (882458 downstream)																																			---	---	---	---
EYS	346007	broad.mit.edu	37	6	64614225	64614225	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64614225delT	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	65148376	65148376	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:65148376delA	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	66111290	66111290	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66111290delT	uc011dxu.1	-						EYS_uc003peq.2_Intron|EYS_uc003per.1_Intron	NM_001142800	NP_001136272			eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6																		---	---	---	---
EYS	346007	broad.mit.edu	37	6	66154984	66154985	+	Intron	DEL	AA	-	-	rs34222132		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66154984_66154985delAA	uc011dxu.1	-						EYS_uc003peq.2_Intron|EYS_uc003per.1_Intron	NM_001142800	NP_001136272			eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	68644512	68644512	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:68644512delA								None (None upstream) : BAI3 (701120 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	68737448	68737448	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:68737448delA								None (None upstream) : BAI3 (608184 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	69014556	69014557	+	IGR	INS	-	A	A	rs34600497		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69014556_69014557insA								None (None upstream) : BAI3 (331075 downstream)																																			---	---	---	---
LMBRD1	55788	broad.mit.edu	37	6	70422333	70422333	+	Intron	DEL	T	-	-	rs140548915		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70422333delT	uc003pfa.2	-						LMBRD1_uc003pey.2_Intron|LMBRD1_uc003pez.2_Intron|LMBRD1_uc010kal.2_Intron|LMBRD1_uc003pfb.2_Intron	NM_018368	NP_060838			liver regeneration p-53 related protein						interspecies interaction between organisms|transport	integral to membrane|lysosomal membrane	cobalamin binding			ovary(1)	1																		---	---	---	---
SMAP1	60682	broad.mit.edu	37	6	71423869	71423869	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71423869delT	uc003pfr.2	+						SMAP1_uc011dxy.1_Intron|SMAP1_uc003pfs.2_Intron|SMAP1_uc010kao.2_Intron|SMAP1_uc010kap.2_Intron	NM_001044305	NP_001037770			stromal membrane-associated GTPase-activating						regulation of ARF GTPase activity	plasma membrane	ARF GTPase activator activity|zinc ion binding				0																		---	---	---	---
SMAP1	60682	broad.mit.edu	37	6	71433908	71433908	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71433908delT	uc003pfr.2	+						SMAP1_uc011dxy.1_Intron|SMAP1_uc003pfs.2_Intron|SMAP1_uc010kao.2_Intron|SMAP1_uc010kap.2_Intron	NM_001044305	NP_001037770			stromal membrane-associated GTPase-activating						regulation of ARF GTPase activity	plasma membrane	ARF GTPase activator activity|zinc ion binding				0																		---	---	---	---
RIMS1	22999	broad.mit.edu	37	6	72961939	72961939	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72961939delG	uc003pga.2	+						RIMS1_uc011dyb.1_Intron|RIMS1_uc003pgc.2_Intron|RIMS1_uc010kaq.2_Intron|RIMS1_uc011dyc.1_Intron|RIMS1_uc010kar.2_Intron|RIMS1_uc011dyd.1_Intron|RIMS1_uc003pgf.2_Intron|RIMS1_uc003pgg.2_Intron|RIMS1_uc003pgi.2_Intron|RIMS1_uc003pgh.2_Intron|RIMS1_uc003pgd.2_Intron|RIMS1_uc003pge.2_Intron|RIMS1_uc011dye.1_5'Flank|RIMS1_uc003pgb.3_Intron|RIMS1_uc010kas.1_Intron	NM_014989	NP_055804			regulating synaptic membrane exocytosis 1						calcium ion-dependent exocytosis|cellular membrane fusion|glutamate secretion|intracellular protein transport|protein complex assembly|regulated secretory pathway|response to stimulus|synaptic vesicle exocytosis|visual perception	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(7)|pancreas(2)|breast(1)	10		all_epithelial(107;0.179)|all_hematologic(105;0.212)																---	---	---	---
KCNQ5	56479	broad.mit.edu	37	6	73407928	73407928	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73407928delT	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	73431010	73431010	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73431010delT	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	73635731	73635731	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73635731delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	74235051	74235051	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74235051delT								EEF1A1 (3760 upstream) : SLC17A5 (68052 downstream)																																			---	---	---	---
SLC17A5	26503	broad.mit.edu	37	6	74312866	74312867	+	Intron	DEL	TT	-	-	rs74916771		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74312866_74312867delTT	uc003phn.3	-						SLC17A5_uc010kax.2_Intron|SLC17A5_uc010kay.2_Intron|SLC17A5_uc011dyo.1_Intron	NM_012434	NP_036566			sialin						anion transport	integral to plasma membrane|lysosomal membrane|membrane fraction	sialic acid:hydrogen symporter activity			skin(5)|central_nervous_system(1)	6																		---	---	---	---
CD109	135228	broad.mit.edu	37	6	74409270	74409270	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74409270delT	uc003php.2	+						CD109_uc010kaz.2_Intron|CD109_uc003phq.2_Intron|CD109_uc010kba.2_Intron	NM_133493	NP_598000			CD109 antigen isoform 1 precursor							anchored to membrane|extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			large_intestine(2)|ovary(2)	4																		---	---	---	---
CD109	135228	broad.mit.edu	37	6	74499823	74499825	+	Intron	DEL	TTT	-	-	rs112037686		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74499823_74499825delTTT	uc003php.2	+						CD109_uc010kaz.2_Intron|CD109_uc003phq.2_Intron|CD109_uc010kba.2_Intron	NM_133493	NP_598000			CD109 antigen isoform 1 precursor							anchored to membrane|extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			large_intestine(2)|ovary(2)	4																		---	---	---	---
CD109	135228	broad.mit.edu	37	6	74509742	74509742	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74509742delT	uc003php.2	+						CD109_uc010kaz.2_Intron|CD109_uc003phq.2_Intron|CD109_uc010kba.2_Intron	NM_133493	NP_598000			CD109 antigen isoform 1 precursor							anchored to membrane|extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			large_intestine(2)|ovary(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	74586119	74586121	+	IGR	DEL	ACA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74586119_74586121delACA								CD109 (48079 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	74713025	74713025	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74713025delA								CD109 (174985 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	75234026	75234026	+	Intron	DEL	T	-	-	rs76131279	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75234026delT	uc003phr.2	+											Homo sapiens full length insert cDNA clone ZD50H02.																														---	---	---	---
COL12A1	1303	broad.mit.edu	37	6	75874987	75874987	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75874987delA	uc003phs.2	-						COL12A1_uc003pht.2_Intron	NM_004370	NP_004361			collagen, type XII, alpha 1 long isoform						cell adhesion|collagen fibril organization|skeletal system development	collagen type XII|extracellular space	extracellular matrix structural constituent conferring tensile strength			ovary(6)|large_intestine(1)|breast(1)|skin(1)	9																		---	---	---	---
TMEM30A	55754	broad.mit.edu	37	6	75995602	75995602	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75995602delT	uc003phw.2	-						TMEM30A_uc003phx.2_5'Flank|uc010kbd.1_Intron	NM_018247	NP_060717			transmembrane protein 30A isoform 1							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	77954646	77954646	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:77954646delT								None (None upstream) : HTR1B (217302 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	78766781	78766781	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:78766781delT								HTR1B (593661 upstream) : IRAK1BP1 (810408 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	79112889	79112889	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79112889delT								HTR1B (939769 upstream) : IRAK1BP1 (464300 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	79426967	79426967	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79426967delA								None (None upstream) : IRAK1BP1 (150222 downstream)																																			---	---	---	---
PHIP	55023	broad.mit.edu	37	6	79680100	79680100	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79680100delA	uc003pir.2	-						PHIP_uc003piq.2_Intron|PHIP_uc011dyp.1_Intron	NM_017934	NP_060404			pleckstrin homology domain interacting protein						insulin receptor signaling pathway|negative regulation of apoptosis|positive regulation of cell proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis	nucleus	insulin receptor binding			large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)	6		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)														---	---	---	---
PHIP	55023	broad.mit.edu	37	6	79708254	79708254	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79708254delA	uc003pir.2	-						PHIP_uc011dyp.1_Intron	NM_017934	NP_060404			pleckstrin homology domain interacting protein						insulin receptor signaling pathway|negative regulation of apoptosis|positive regulation of cell proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis	nucleus	insulin receptor binding			large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)	6		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)														---	---	---	---
HMGN3	9324	broad.mit.edu	37	6	79911547	79911548	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79911547_79911548delTT	uc003pit.2	-						HMGN3_uc003pis.2_Intron|HMGN3_uc003piu.1_3'UTR	NM_004242	NP_004233			high mobility group nucleosomal binding domain 3						chromatin modification	chromatin|cytoplasm|nucleus	DNA binding|thyroid hormone receptor binding				0		all_cancers(76;0.000116)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0393)		BRCA - Breast invasive adenocarcinoma(397;0.125)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	80017193	80017193	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80017193delT								HMGN3 (72738 upstream) : LCA5 (177516 downstream)																																			---	---	---	---
BCKDHB	594	broad.mit.edu	37	6	81013368	81013369	+	Intron	DEL	GT	-	-	rs76653318	byFrequency;by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:81013368_81013369delGT	uc003pjd.2	+						BCKDHB_uc003pje.2_Intron	NM_000056	NP_000047			branched chain keto acid dehydrogenase E1 beta						branched chain family amino acid catabolic process	mitochondrial alpha-ketoglutarate dehydrogenase complex	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity|carboxy-lyase activity|protein binding				0		all_cancers(76;1.38e-05)|Acute lymphoblastic leukemia(125;1.15e-05)|all_hematologic(105;0.00118)|all_epithelial(107;0.0149)		BRCA - Breast invasive adenocarcinoma(397;0.0291)														---	---	---	---
BCKDHB	594	broad.mit.edu	37	6	81036593	81036593	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:81036593delA	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	82752452	82752452	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82752452delT								FAM46A (290024 upstream) : IBTK (127504 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	83001169	83001170	+	IGR	DEL	AA	-	-	rs112864435		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83001169_83001170delAA								IBTK (43721 upstream) : TPBG (71753 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	83574290	83574290	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83574290delA								TPBG (497676 upstream) : UBE2CBP (27896 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	83591386	83591386	+	IGR	DEL	A	-	-	rs138289976		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83591386delA								TPBG (514772 upstream) : UBE2CBP (10800 downstream)																																			---	---	---	---
DOPEY1	23033	broad.mit.edu	37	6	83840469	83840469	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83840469delT	uc003pjs.1	+						DOPEY1_uc011dyy.1_Intron|DOPEY1_uc010kbl.1_Intron	NM_015018	NP_055833			dopey family member 1						protein transport					ovary(2)|breast(1)|central_nervous_system(1)	4		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	84238856	84238856	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84238856delT								PRSS35 (3437 upstream) : SNAP91 (23751 downstream)																																			---	---	---	---
MRAP2	112609	broad.mit.edu	37	6	84785783	84785784	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84785783_84785784delTT	uc003pkg.3	+						MRAP2_uc010kbo.2_Intron	NM_138409	NP_612418			melanocortin 2 receptor accessory protein 2						positive regulation of cAMP biosynthetic process|protein localization at cell surface	endoplasmic reticulum|plasma membrane	corticotropin hormone receptor binding|type 1 melanocortin receptor binding|type 3 melanocortin receptor binding|type 4 melanocortin receptor binding|type 5 melanocortin receptor binding			skin(2)	2																		---	---	---	---
SNX14	57231	broad.mit.edu	37	6	86269887	86269888	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86269887_86269888insA	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)														---	---	---	---
SNHG5	387066	broad.mit.edu	37	6	86386983	86386983	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86386983delA	uc003plb.3	-						SNHG5_uc003plc.3_Intron|SNHG5_uc003pld.3_Intron|SNHG5_uc003plf.2_RNA					Homo sapiens chromosome 6 open reading frame 160, mRNA (cDNA clone IMAGE:3927795).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	86486192	86486192	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86486192delA								SNHG5 (97741 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	86970083	86970084	+	IGR	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86970083_86970084delGT								SNHG5 (581632 upstream) : HTR1E (676940 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	87821431	87821431	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87821431delT								CGA (16607 upstream) : ZNF292 (41120 downstream)																																			---	---	---	---
C6orf164	63914	broad.mit.edu	37	6	88071007	88071007	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88071007delA	uc003plr.2	+						C6orf163_uc003pls.2_Intron					Homo sapiens DC18 mRNA, complete cds.												0																		---	---	---	---
RARS2	57038	broad.mit.edu	37	6	88240359	88240359	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88240359delA	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)														---	---	---	---
ORC3L	23595	broad.mit.edu	37	6	88361041	88361041	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88361041delA	uc003pmh.2	+						ORC3L_uc011dzl.1_Intron|ORC3L_uc011dzm.1_Intron|ORC3L_uc011dzn.1_RNA|ORC3L_uc003pmg.2_Intron|ORC3L_uc003pmi.2_Intron|ORC3L_uc011dzo.1_Intron|ORC3L_uc011dzp.1_Intron	NM_012381	NP_036513			origin recognition complex, subunit 3 isoform 2						cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	nuclear origin of replication recognition complex|nucleoplasm	DNA replication origin binding|protein binding				0		all_cancers(76;9.05e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;5.29e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.0469)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	88432819	88432819	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88432819delT								AKIRIN2 (20834 upstream) : SPACA1 (324688 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	88994140	88994141	+	IGR	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88994140_88994141delGT								CNR1 (118373 upstream) : RNGTT (325848 downstream)																																			---	---	---	---
RNGTT	8732	broad.mit.edu	37	6	89581698	89581698	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89581698delT	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	90139201	90139201	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90139201delT								RRAGD (17206 upstream) : ANKRD6 (3696 downstream)																																			---	---	---	---
MDN1	23195	broad.mit.edu	37	6	90447743	90447743	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90447743delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	91180460	91180460	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91180460delT								BACH2 (173898 upstream) : MAP3K7 (44893 downstream)																																			---	---	---	---
MAP3K7	6885	broad.mit.edu	37	6	91246268	91246269	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91246268_91246269delAA	uc003pnz.1	-						MAP3K7_uc003pny.1_5'UTR|MAP3K7_uc003poa.1_Intron|MAP3K7_uc003pob.1_Intron|MAP3K7_uc003poc.1_Intron	NM_145331	NP_663304			mitogen-activated protein kinase kinase kinase 7						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	91569399	91569400	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91569399_91569400delTC								MAP3K7 (272492 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	91569401	91569406	+	IGR	DEL	TTTTTT	-	-	rs67389161		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91569401_91569406delTTTTTT								MAP3K7 (272494 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	92368582	92368582	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92368582delT	uc003pod.2	-											Homo sapiens cDNA clone IMAGE:5284581.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	92394623	92394624	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92394623_92394624delAC	uc003pod.2	-											Homo sapiens cDNA clone IMAGE:5284581.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	93254043	93254044	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93254043_93254044delTG								None (None upstream) : EPHA7 (695698 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	93851362	93851362	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93851362delG								None (None upstream) : EPHA7 (98380 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	94950652	94950652	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:94950652delA								TSG1 (464453 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	95355310	95355310	+	IGR	DEL	T	-	-	rs71730592		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:95355310delT								TSG1 (869111 upstream) : MANEA (670103 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	95881232	95881234	+	IGR	DEL	ATC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:95881232_95881234delATC								None (None upstream) : MANEA (144179 downstream)																																			---	---	---	---
MANEA	79694	broad.mit.edu	37	6	96040806	96040806	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96040806delA	uc003poo.1	+							NM_024641	NP_078917			mannosidase, endo-alpha						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	glycoprotein endo-alpha-1,2-mannosidase activity			ovary(2)|breast(1)	3		all_cancers(76;1.01e-06)|Acute lymphoblastic leukemia(125;3.58e-09)|all_hematologic(75;1.22e-06)|all_epithelial(107;0.00433)|Colorectal(196;0.0341)		BRCA - Breast invasive adenocarcinoma(108;0.148)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	96225803	96225803	+	IGR	DEL	T	-	-	rs79546134		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96225803delT								MANEA (168477 upstream) : FUT9 (238042 downstream)																																			---	---	---	---
FUT9	10690	broad.mit.edu	37	6	96566194	96566194	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96566194delA	uc003pop.3	+							NM_006581	NP_006572			fucosyltransferase 9 (alpha (1,3)						L-fucose catabolic process|protein glycosylation	Golgi cisterna membrane|integral to membrane	alpha(1,3)-fucosyltransferase activity			skin(4)|ovary(1)	5		all_cancers(76;4.77e-07)|Acute lymphoblastic leukemia(125;4.01e-09)|all_hematologic(75;1.25e-06)|all_epithelial(107;0.00279)|Colorectal(196;0.0356)		BRCA - Breast invasive adenocarcinoma(108;0.08)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	98550380	98550380	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:98550380delT								MIR2113 (77883 upstream) : POU3F2 (732200 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	99419161	99419161	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99419161delG								FBXL4 (23312 upstream) : C6orf168 (301633 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	99483096	99483096	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99483096delA								FBXL4 (87247 upstream) : C6orf168 (237698 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	99672768	99672768	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99672768delT								FBXL4 (276919 upstream) : C6orf168 (48026 downstream)																																			---	---	---	---
COQ3	51805	broad.mit.edu	37	6	99817819	99817820	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99817819_99817820insA	uc003ppk.2	-							NM_017421	NP_059117			hexaprenyldihydroxybenzoate methyltransferase						glycerol metabolic process|ubiquinone biosynthetic process	mitochondrial matrix	2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity|3-demethylubiquinone-9 3-O-methyltransferase activity|hexaprenyldihydroxybenzoate methyltransferase activity			upper_aerodigestive_tract(1)	1		all_cancers(76;1.24e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.00716)|Colorectal(196;0.0691)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0625)														---	---	---	---
SFRS18	25957	broad.mit.edu	37	6	99852665	99852665	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99852665delT	uc003ppo.3	-						SFRS18_uc003ppp.3_Intron|SFRS18_uc011eag.1_Intron	NM_032870	NP_116259			splicing factor, arginine/serine-rich 130							nuclear speck					0		all_cancers(76;1.24e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.00716)|Colorectal(196;0.0691)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0631)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	100544545	100544545	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100544545delA								MCHR2 (102431 upstream) : SIM1 (292206 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	100653039	100653039	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100653039delA								MCHR2 (210925 upstream) : SIM1 (183712 downstream)																																			---	---	---	---
ASCC3	10973	broad.mit.edu	37	6	101172163	101172163	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101172163delA	uc003pqk.2	-						ASCC3_uc011eai.1_Intron|ASCC3_uc003pql.2_Intron	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)														---	---	---	---
ASCC3	10973	broad.mit.edu	37	6	101269400	101269400	+	Intron	DEL	A	-	-	rs9498398		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101269400delA	uc003pqk.2	-						ASCC3_uc011eai.1_Intron|ASCC3_uc003pql.2_Intron	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)														---	---	---	---
ASCC3	10973	broad.mit.edu	37	6	101296336	101296336	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101296336delA	uc003pqk.2	-	4	818	c.489delT	c.(487-489)TTTfs	p.F163fs	ASCC3_uc011eai.1_Frame_Shift_Del_p.F65fs|ASCC3_uc003pql.2_Frame_Shift_Del_p.F163fs|ASCC3_uc010kcv.2_Frame_Shift_Del_p.F163fs	NM_006828	NP_006819	Q8N3C0	HELC1_HUMAN	activating signal cointegrator 1 complex subunit	163					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	101560479	101560479	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101560479delA								ASCC3 (231255 upstream) : GRIK2 (286426 downstream)																																			---	---	---	---
GRIK2	2898	broad.mit.edu	37	6	102383941	102383941	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:102383941delT	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	103088612	103088613	+	IGR	INS	-	TGTGTG	TGTGTG	rs149683184	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:103088612_103088613insTGTGTG								GRIK2 (570655 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	104163900	104163900	+	IGR	DEL	T	-	-	rs75776371		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:104163900delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	104378614	104378614	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:104378614delT								None (None upstream) : HACE1 (797354 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	104551543	104551543	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:104551543delA								None (None upstream) : HACE1 (624425 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	105935834	105935835	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105935834_105935835delAA								PREP (84865 upstream) : PRDM1 (598360 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	105993923	105993923	+	IGR	DEL	T	-	-	rs72157707		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105993923delT								PREP (142954 upstream) : PRDM1 (540272 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	106150904	106150904	+	IGR	DEL	T	-	-	rs113241614		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106150904delT								PREP (299935 upstream) : PRDM1 (383291 downstream)																																			---	---	---	---
RTN4IP1	84816	broad.mit.edu	37	6	107040240	107040240	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107040240delA	uc003prj.2	-						RTN4IP1_uc010kdd.2_Intron|RTN4IP1_uc003prk.2_Intron	NM_032730	NP_116119			reticulon 4 interacting protein 1 precursor							mitochondrion	oxidoreductase activity|zinc ion binding				0	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;9.45e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0144)	Epithelial(6;0.000873)|all cancers(7;0.00363)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0394)	all cancers(137;0.113)|BRCA - Breast invasive adenocarcinoma(108;0.127)|Epithelial(106;0.144)														---	---	---	---
QRSL1	55278	broad.mit.edu	37	6	107108480	107108482	+	Intron	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107108480_107108482delTTT	uc003prm.2	+							NM_018292	NP_060762			glutaminyl-tRNA synthase						translation		ATP binding|carbon-nitrogen ligase activity, with glutamine as amido-N-donor				0	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;0.00768)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.248)	Epithelial(6;0.000334)|all cancers(7;0.00157)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0152)	BRCA - Breast invasive adenocarcinoma(108;0.118)|all cancers(137;0.167)|Epithelial(106;0.176)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	107331443	107331444	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107331443_107331444delAA								MIR587 (99348 upstream) : C6orf203 (17963 downstream)																																			---	---	---	---
PDSS2	57107	broad.mit.edu	37	6	107576403	107576404	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107576403_107576404delTT	uc003prt.2	-						PDSS2_uc011eak.1_Intron|PDSS2_uc011eal.1_Intron|PDSS2_uc003pru.2_Intron	NM_020381	NP_065114			prenyl diphosphate synthase, subunit 2						isoprenoid biosynthetic process|ubiquinone biosynthetic process	mitochondrion	protein heterodimerization activity			ovary(2)	2	Breast(9;0.0127)	all_cancers(87;3.63e-05)|Acute lymphoblastic leukemia(125;2.86e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.0108)|Colorectal(196;0.156)|Lung NSC(302;0.211)	BRCA - Breast invasive adenocarcinoma(8;0.0101)|all cancers(7;0.243)	BRCA - Breast invasive adenocarcinoma(108;0.112)|OV - Ovarian serous cystadenocarcinoma(136;0.173)|all cancers(137;0.191)														---	---	---	---
SOBP	55084	broad.mit.edu	37	6	107956439	107956439	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107956439delG	uc003prx.2	+	6	2895	c.2391delG	c.(2389-2391)GCGfs	p.A797fs		NM_018013	NP_060483	A7XYQ1	SOBP_HUMAN	sine oculis binding protein homolog	797							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	108346181	108346188	+	IGR	DEL	TTTGTTTG	-	-	rs10601238		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108346181_108346188delTTTGTTTG								SEC63 (66699 upstream) : OSTM1 (16427 downstream)																																			---	---	---	---
SNX3	8724	broad.mit.edu	37	6	108533549	108533549	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108533549delT	uc003psh.2	-						SNX3_uc003psi.2_Intron|SNX3_uc010kdi.2_Intron	NM_003795	NP_003786			sorting nexin 3 isoform a						cell communication|endocytosis|protein transport	early endosome|endosome membrane	phosphatidylinositol-3-phosphate binding|protein phosphatase binding				0		all_cancers(87;3.82e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000195)|Colorectal(196;0.0293)|all_lung(197;0.0938)		BRCA - Breast invasive adenocarcinoma(108;0.0136)|Epithelial(106;0.0564)|OV - Ovarian serous cystadenocarcinoma(136;0.0717)|all cancers(137;0.0743)														---	---	---	---
LACE1	246269	broad.mit.edu	37	6	108723558	108723558	+	Intron	DEL	T	-	-	rs112384144		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108723558delT	uc003psj.2	+							NM_145315	NP_660358			lactation elevated 1								ATP binding			central_nervous_system(1)	1		all_cancers(87;1.5e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;6.79e-05)|Colorectal(196;0.0294)|all_lung(197;0.0486)|Lung SC(18;0.152)		BRCA - Breast invasive adenocarcinoma(108;0.00179)|Epithelial(106;0.0024)|all cancers(137;0.00379)|OV - Ovarian serous cystadenocarcinoma(136;0.0118)														---	---	---	---
LACE1	246269	broad.mit.edu	37	6	108797969	108797969	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108797969delT	uc003psj.2	+							NM_145315	NP_660358			lactation elevated 1								ATP binding			central_nervous_system(1)	1		all_cancers(87;1.5e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;6.79e-05)|Colorectal(196;0.0294)|all_lung(197;0.0486)|Lung SC(18;0.152)		BRCA - Breast invasive adenocarcinoma(108;0.00179)|Epithelial(106;0.0024)|all cancers(137;0.00379)|OV - Ovarian serous cystadenocarcinoma(136;0.0118)														---	---	---	---
LACE1	246269	broad.mit.edu	37	6	108843371	108843371	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108843371delA	uc003psj.2	+							NM_145315	NP_660358			lactation elevated 1								ATP binding			central_nervous_system(1)	1		all_cancers(87;1.5e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;6.79e-05)|Colorectal(196;0.0294)|all_lung(197;0.0486)|Lung SC(18;0.152)		BRCA - Breast invasive adenocarcinoma(108;0.00179)|Epithelial(106;0.0024)|all cancers(137;0.00379)|OV - Ovarian serous cystadenocarcinoma(136;0.0118)														---	---	---	---
ARMC2	84071	broad.mit.edu	37	6	109291241	109291241	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109291241delA	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	109356752	109356752	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109356752delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	109614819	109614819	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109614819delT	uc003ptb.1	+						uc010kdm.1_5'Flank					RecName: Full=Uncharacterized protein C6orf184;																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	111296806	111296808	+	IGR	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111296806_111296808delTTT								GTF3C6 (7717 upstream) : RPF2 (6483 downstream)																																			---	---	---	---
REV3L	5980	broad.mit.edu	37	6	111678896	111678897	+	Intron	DEL	AA	-	-	rs80203385		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111678896_111678897delAA	uc003puy.3	-						REV3L_uc003pux.3_Intron|REV3L_uc003puz.3_Intron|REV3L_uc003pva.1_Intron	NM_002912	NP_002903			DNA polymerase zeta						DNA-dependent DNA replication|translesion synthesis	nucleus|zeta DNA polymerase complex	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding			large_intestine(2)|ovary(2)|skin(2)	6		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)									DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
REV3L	5980	broad.mit.edu	37	6	111680317	111680317	+	Intron	DEL	A	-	-	rs75315187		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111680317delA	uc003puy.3	-						REV3L_uc003pux.3_Intron|REV3L_uc003puz.3_Intron|REV3L_uc003pva.1_Intron	NM_002912	NP_002903			DNA polymerase zeta						DNA-dependent DNA replication|translesion synthesis	nucleus|zeta DNA polymerase complex	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding			large_intestine(2)|ovary(2)|skin(2)	6		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)									DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
Unknown	0	broad.mit.edu	37	6	113173719	113173719	+	IGR	DEL	A	-	-	rs113156193		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:113173719delA								RFPL4B (501221 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	113511569	113511570	+	IGR	DEL	CA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:113511569_113511570delCA								RFPL4B (839071 upstream) : MARCKS (666957 downstream)																																			---	---	---	---
HS3ST5	222537	broad.mit.edu	37	6	114378234	114378234	+	3'UTR	DEL	T	-	-	rs80329057		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114378234delT	uc003pwg.3	-	2					uc003pwf.2_Intron|HS3ST5_uc003pwh.3_3'UTR	NM_153612	NP_705840			heparan sulfate (glucosamine)						heparan sulfate proteoglycan biosynthetic process, enzymatic modification|negative regulation of coagulation|protein sulfation|regulation of virion penetration into host cell	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity|protein binding			ovary(1)|pancreas(1)	2		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)														---	---	---	---
HS3ST5	222537	broad.mit.edu	37	6	114598379	114598379	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114598379delT	uc003pwh.3	-						uc003pwf.2_Intron	NM_153612	NP_705840			heparan sulfate (glucosamine)						heparan sulfate proteoglycan biosynthetic process, enzymatic modification|negative regulation of coagulation|protein sulfation|regulation of virion penetration into host cell	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity|protein binding			ovary(1)|pancreas(1)	2		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)														---	---	---	---
HS3ST5	222537	broad.mit.edu	37	6	114641595	114641595	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114641595delA	uc003pwh.3	-						uc003pwf.2_Intron	NM_153612	NP_705840			heparan sulfate (glucosamine)						heparan sulfate proteoglycan biosynthetic process, enzymatic modification|negative regulation of coagulation|protein sulfation|regulation of virion penetration into host cell	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity|protein binding			ovary(1)|pancreas(1)	2		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	114921524	114921524	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114921524delT								HS3ST5 (257984 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	115013229	115013230	+	IGR	INS	-	A	A	rs139322882	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:115013229_115013230insA								HS3ST5 (349689 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	115941179	115941180	+	IGR	DEL	CA	-	-	rs72219737		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:115941179_115941180delCA								None (None upstream) : FRK (321513 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	116058648	116058649	+	IGR	DEL	CA	-	-	rs112275057		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116058648_116058649delCA								None (None upstream) : FRK (204044 downstream)																																			---	---	---	---
DSE	29940	broad.mit.edu	37	6	116615721	116615721	+	Intron	DEL	G	-	-	rs71554846		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116615721delG	uc003pws.2	+						DSE_uc011ebf.1_Intron|DSE_uc003pwq.1_Intron|DSE_uc003pwr.2_Intron	NM_001080976	NP_001074445			dermatan sulfate epimerase precursor						dermatan sulfate biosynthetic process	endoplasmic reticulum|Golgi apparatus|integral to membrane	chondroitin-glucuronate 5-epimerase activity			ovary(1)	1		all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234)		Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262)														---	---	---	---
RWDD1	51389	broad.mit.edu	37	6	116910213	116910213	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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	117299545	117299545	+	IGR	DEL	T	-	-	rs111812646		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117299545delT								RFX6 (46237 upstream) : VGLL2 (287176 downstream)																																			---	---	---	---
ROS1	6098	broad.mit.edu	37	6	117686253	117686253	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117686253delT	uc003pxp.1	-	20	3287	c.3088delA	c.(3088-3090)ACAfs	p.T1030fs	ROS1_uc011ebi.1_RNA|GOPC_uc003pxq.1_Intron	NM_002944	NP_002935	P08922	ROS_HUMAN	proto-oncogene c-ros-1 protein precursor	1030	Fibronectin type-III 4.|Extracellular (Potential).				transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(8)|ovary(6)|central_nervous_system(3)|skin(3)|stomach(2)|breast(2)|large_intestine(1)	25		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)				T	GOPC|ROS1	glioblastoma|NSCLC								---	---	---	---
MCM9	254394	broad.mit.edu	37	6	119245399	119245399	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119245399delA	uc003pyh.2	-							NM_153255	NP_694987			minichromosome maintenance complex component 9						DNA replication		ATP binding|DNA binding|nucleoside-triphosphatase activity			ovary(1)	1		all_cancers(87;0.122)|all_epithelial(87;0.179)		GBM - Glioblastoma multiforme(226;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.194)														---	---	---	---
FAM184A	79632	broad.mit.edu	37	6	119317648	119317648	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119317648delT	uc003pyj.2	-						FAM184A_uc003pyk.3_Intron|FAM184A_uc003pyl.3_Intron	NM_024581	NP_078857			hypothetical protein LOC79632 isoform 1											ovary(2)|central_nervous_system(2)|skin(2)|pancreas(1)	7																		---	---	---	---
MAN1A1	4121	broad.mit.edu	37	6	119596282	119596282	+	Intron	DEL	T	-	-	rs4945633	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119596282delT	uc003pym.1	-						MAN1A1_uc010kei.1_Intron	NM_005907	NP_005898			mannosidase, alpha, class 1A, member 1						post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum|ER-Golgi intermediate compartment|Golgi membrane|integral to membrane|membrane fraction	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			ovary(2)|central_nervous_system(1)|skin(1)	4		all_epithelial(87;0.173)		OV - Ovarian serous cystadenocarcinoma(136;0.0612)|GBM - Glioblastoma multiforme(226;0.0702)|all cancers(137;0.115)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	119772987	119772987	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119772987delG								MAN1A1 (102061 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	119990250	119990250	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119990250delA								MAN1A1 (319324 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	120014628	120014628	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:120014628delT								MAN1A1 (343702 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	120579497	120579502	+	IGR	DEL	GTGTGC	-	-	rs72558271	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:120579497_120579502delGTGTGC								MAN1A1 (908571 upstream) : C6orf170 (821125 downstream)																																			---	---	---	---
C6orf170	221322	broad.mit.edu	37	6	121629008	121629009	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121629008_121629009insA	uc003pyo.1	-						C6orf170_uc003pyq.1_Intron	NM_152730	NP_689943			hypothetical protein LOC221322						multicellular organismal development	cilium|cytoplasm	Rab GTPase activator activity			central_nervous_system(2)|ovary(1)	3				GBM - Glioblastoma multiforme(226;0.00521)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	122179387	122179387	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122179387delT								GJA1 (408515 upstream) : HSF2 (541309 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	122279277	122279277	+	IGR	DEL	A	-	-	rs5879619		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122279277delA								GJA1 (508405 upstream) : HSF2 (441419 downstream)																																			---	---	---	---
FABP7	2173	broad.mit.edu	37	6	123101679	123101679	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123101679delT	uc003pzf.2	+						FABP7_uc003pzd.2_Intron|FABP7_uc003pze.1_3'UTR	NM_001446	NP_001437			fatty acid binding protein 7, brain						negative regulation of cell proliferation	cytoplasm	lipid binding|transporter activity				0				GBM - Glioblastoma multiforme(226;0.226)	Alpha-Linolenic Acid(DB00132)|gamma-Homolinolenic acid(DB00154)|Icosapent(DB00159)													---	---	---	---
TRDN	10345	broad.mit.edu	37	6	123589099	123589100	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123589099_123589100insT	uc003pzj.1	-						TRDN_uc010kem.1_Intron	NM_006073	NP_006064			triadin						muscle contraction	integral to membrane|plasma membrane|sarcoplasmic reticulum membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.184)														---	---	---	---
TRDN	10345	broad.mit.edu	37	6	123680655	123680655	+	Intron	DEL	A	-	-	rs147851228		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123680655delA	uc003pzj.1	-						TRDN_uc003pzk.1_Intron|TRDN_uc003pzl.1_Intron|TRDN_uc010kem.1_Intron	NM_006073	NP_006064			triadin						muscle contraction	integral to membrane|plasma membrane|sarcoplasmic reticulum membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.184)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	124008716	124008717	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124008716_124008717delAA								TRDN (50774 upstream) : NKAIN2 (116352 downstream)																																			---	---	---	---
NKAIN2	154215	broad.mit.edu	37	6	124515463	124515463	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124515463delT	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	124799663	124799664	+	Intron	DEL	CA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124799663_124799664delCA	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	125429711	125429712	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125429711_125429712insT								RNF217 (25054 upstream) : TPD52L1 (45167 downstream)																																			---	---	---	---
TPD52L1	7164	broad.mit.edu	37	6	125479718	125479720	+	Intron	DEL	GAG	-	-	rs143758443		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125479718_125479720delGAG	uc003pzu.1	+						TPD52L1_uc003pzv.1_Intron|TPD52L1_uc003pzw.1_Intron|TPD52L1_uc003pzx.1_Intron|TPD52L1_uc003pzy.1_Intron	NM_003287	NP_003278			tumor protein D52-like 1 isoform 1						DNA fragmentation involved in apoptotic nuclear change|G2/M transition of mitotic cell cycle|induction of apoptosis|positive regulation of JNK cascade|positive regulation of MAP kinase activity	perinuclear region of cytoplasm	caspase activator activity|protein heterodimerization activity|protein homodimerization activity				0			LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828)	GBM - Glioblastoma multiforme(226;0.0265)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	126618458	126618458	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126618458delT								TRMT11 (258040 upstream) : CENPW (42795 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	126620099	126620099	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126620099delT								TRMT11 (259681 upstream) : CENPW (41154 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	126729412	126729412	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126729412delA	uc003qaq.1	-						CENPW_uc003qap.3_Intron					Homo sapiens cDNA FLJ45564 fis, clone BRTHA3007469.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	127097969	127097970	+	Intron	DEL	AA	-	-	rs79399440		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127097969_127097970delAA	uc003qaq.1	-											Homo sapiens cDNA FLJ45564 fis, clone BRTHA3007469.																														---	---	---	---
RSPO3	84870	broad.mit.edu	37	6	127470740	127470740	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127470740delA	uc003qar.2	+						RSPO3_uc003qas.1_Intron	NM_032784	NP_116173			R-spondin 3 precursor							extracellular region	heparin binding				0				GBM - Glioblastoma multiforme(226;0.0555)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	127758952	127758952	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127758952delT								ECHDC1 (94198 upstream) : C6orf174 (600 downstream)																																			---	---	---	---
C6orf174	387104	broad.mit.edu	37	6	127795735	127795735	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127795735delT	uc003qbd.2	-						C6orf174_uc003qbc.2_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)														---	---	---	---
PTPRK	5796	broad.mit.edu	37	6	128321487	128321487	+	Intron	DEL	A	-	-	rs113113294		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128321487delA	uc003qbk.2	-						PTPRK_uc003qbj.2_Intron|PTPRK_uc010kfc.2_Intron|PTPRK_uc011ebu.1_Intron|PTPRK_uc003qbl.1_Intron|PTPRK_uc011ebv.1_Intron|PTPRK_uc010kfd.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)														---	---	---	---
LAMA2	3908	broad.mit.edu	37	6	129238845	129238845	+	Intron	DEL	T	-	-	rs113304257		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129238845delT	uc003qbn.2	+						LAMA2_uc003qbo.2_Intron	NM_000426	NP_000417			laminin alpha 2 subunit isoform a precursor						cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)														---	---	---	---
LAMA2	3908	broad.mit.edu	37	6	129495630	129495631	+	Intron	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129495630_129495631delGT	uc003qbn.2	+						LAMA2_uc003qbo.2_Intron	NM_000426	NP_000417			laminin alpha 2 subunit isoform a precursor						cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)														---	---	---	---
LAMA2	3908	broad.mit.edu	37	6	129565873	129565873	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129565873delA	uc003qbn.2	+						LAMA2_uc003qbo.2_Intron	NM_000426	NP_000417			laminin alpha 2 subunit isoform a precursor						cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)														---	---	---	---
LAMA2	3908	broad.mit.edu	37	6	129626966	129626966	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129626966delT	uc003qbn.2	+						LAMA2_uc003qbo.2_Intron	NM_000426	NP_000417			laminin alpha 2 subunit isoform a precursor						cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)														---	---	---	---
LAMA2	3908	broad.mit.edu	37	6	129652800	129652800	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129652800delT	uc003qbn.2	+						LAMA2_uc003qbo.2_Intron	NM_000426	NP_000417			laminin alpha 2 subunit isoform a precursor						cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)														---	---	---	---
LAMA2	3908	broad.mit.edu	37	6	129708197	129708198	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129708197_129708198delAA	uc003qbn.2	+						LAMA2_uc003qbo.2_Intron	NM_000426	NP_000417			laminin alpha 2 subunit isoform a precursor						cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)														---	---	---	---
L3MBTL3	84456	broad.mit.edu	37	6	130425882	130425882	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130425882delA	uc003qbt.2	+						L3MBTL3_uc003qbu.2_Intron	NM_032438	NP_115814			l(3)mbt-like 3 isoform a						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(5)|skin(1)	6				GBM - Glioblastoma multiforme(226;0.0266)|OV - Ovarian serous cystadenocarcinoma(155;0.154)														---	---	---	---
SAMD3	154075	broad.mit.edu	37	6	130577001	130577001	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130577001delT	uc003qbx.2	-							NM_001017373	NP_001017373			sterile alpha motif domain containing 3 isoform											ovary(1)	1				GBM - Glioblastoma multiforme(226;0.00594)|OV - Ovarian serous cystadenocarcinoma(155;0.128)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	130997319	130997319	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130997319delC								TMEM200A (233111 upstream) : LOC285733 (151005 downstream)																																			---	---	---	---
EPB41L2	2037	broad.mit.edu	37	6	131288693	131288693	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131288693delT	uc003qch.2	-						EPB41L2_uc003qcg.1_Intron|EPB41L2_uc011eby.1_Intron|EPB41L2_uc003qci.2_Intron|EPB41L2_uc010kfk.2_Intron|EPB41L2_uc010kfl.1_Intron	NM_001431	NP_001422			erythrocyte membrane protein band 4.1-like 2						cortical actin cytoskeleton organization	extrinsic to membrane|plasma membrane|spectrin	actin binding|structural molecule activity			central_nervous_system(1)|skin(1)	2	Breast(56;0.0639)			OV - Ovarian serous cystadenocarcinoma(155;0.0271)|GBM - Glioblastoma multiforme(226;0.0355)														---	---	---	---
ENPP1	5167	broad.mit.edu	37	6	132139426	132139426	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132139426delA	uc011ecf.1	+							NM_006208	NP_006199			ectonucleotide pyrophosphatase/phosphodiesterase						3'-phosphoadenosine 5'-phosphosulfate metabolic process|biomineral tissue development|cellular phosphate ion homeostasis|cellular response to insulin stimulus|generation of precursor metabolites and energy|immune response|inorganic diphosphate transport|negative regulation of cell growth|negative regulation of fat cell differentiation|negative regulation of glucose import|negative regulation of glycogen biosynthetic process|negative regulation of insulin receptor signaling pathway|negative regulation of protein autophosphorylation|nucleoside triphosphate catabolic process|phosphate metabolic process|sequestering of triglyceride|water-soluble vitamin metabolic process	basolateral plasma membrane|cell surface|extracellular space|integral to membrane	ATP binding|insulin receptor binding|metal ion binding|nucleic acid binding|nucleoside-triphosphate diphosphatase activity|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|protein homodimerization activity|scavenger receptor activity			upper_aerodigestive_tract(2)|ovary(2)	4	Breast(56;0.0505)			GBM - Glioblastoma multiforme(226;0.0216)|OV - Ovarian serous cystadenocarcinoma(155;0.022)	Amifostine(DB01143)|Ribavirin(DB00811)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	133506982	133506982	+	IGR	DEL	T	-	-	rs71764783		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133506982delT								LOC285735 (79272 upstream) : EYA4 (54754 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	134052736	134052737	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134052736_134052737delAC	uc003qeg.1	-											Homo sapiens cDNA FLJ36194 fis, clone TESTI2027615.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	134409573	134409573	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134409573delT								SLC2A12 (35784 upstream) : SGK1 (80812 downstream)																																			---	---	---	---
SGK1	6446	broad.mit.edu	37	6	134588443	134588443	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134588443delT	uc003qeo.3	-						SGK1_uc003qep.2_Intron	NM_001143676	NP_001137148			serum/glucocorticoid regulated kinase 1 isoform						apoptosis|response to stress|sodium ion transport	endoplasmic reticulum|nucleus|plasma membrane	ATP binding|protein binding|protein serine/threonine kinase activity			skin(3)|stomach(1)|lung(1)|central_nervous_system(1)	6	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	134717223	134717224	+	IGR	INS	-	TTCCTTTCTTTTCCC	TTCCTTTCTTTTCCC	rs145645346	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134717223_134717224insTTCCTTTCTTTTCCC								SGK1 (78027 upstream) : ALDH8A1 (521305 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	134746432	134746432	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134746432delT								SGK1 (107236 upstream) : ALDH8A1 (492097 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	135028414	135028414	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135028414delT								SGK1 (389218 upstream) : ALDH8A1 (210115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	135166597	135166599	+	IGR	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135166597_135166599delTTT								SGK1 (527401 upstream) : ALDH8A1 (71930 downstream)																																			---	---	---	---
C6orf217	100131814	broad.mit.edu	37	6	135870915	135870915	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135870915delT	uc003qgn.2	+						C6orf217_uc003qgo.2_Intron|C6orf217_uc010kgo.2_Intron|C6orf217_uc003qgm.2_Intron					Homo sapiens cDNA clone IMAGE:4795512.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	136128475	136128476	+	IGR	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136128475_136128476delAG								C6orf217 (91283 upstream) : PDE7B (44358 downstream)																																			---	---	---	---
MAP3K5	4217	broad.mit.edu	37	6	136883493	136883493	+	Intron	DEL	T	-	-	rs11322947		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136883493delT	uc003qhc.2	-						MAP3K5_uc011edj.1_Intron	NM_005923	NP_005914			mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms		ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding			ovary(2)|skin(2)|lung(1)	5	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)														---	---	---	---
MAP3K5	4217	broad.mit.edu	37	6	137032335	137032335	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137032335delA	uc003qhc.2	-						MAP3K5_uc011edk.1_Intron|MAP3K5_uc010kgw.1_Intron	NM_005923	NP_005914			mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms		ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding			ovary(2)|skin(2)|lung(1)	5	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)														---	---	---	---
PEX7	5191	broad.mit.edu	37	6	137158950	137158951	+	Intron	INS	-	CA	CA	rs62420684	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137158950_137158951insCA	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	137614250	137614254	+	IGR	DEL	TTTTC	-	-	rs1167534		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137614250_137614254delTTTTC								IFNGR1 (73683 upstream) : OLIG3 (199082 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	137879058	137879060	+	IGR	DEL	TTT	-	-	rs77462794		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137879058_137879060delTTT								OLIG3 (63527 upstream) : TNFAIP3 (309521 downstream)																																			---	---	---	---
KIAA1244	57221	broad.mit.edu	37	6	138515406	138515411	+	Intron	DEL	AAAAAA	-	-	rs71758894		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138515406_138515411delAAAAAA	uc003qhu.2	+							NM_020340	NP_065073			brefeldin A-inhibited guanine						regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity			ovary(1)|skin(1)	2	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)														---	---	---	---
KIAA1244	57221	broad.mit.edu	37	6	138564857	138564857	+	Intron	DEL	A	-	-	rs66810600		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138564857delA	uc003qhu.2	+							NM_020340	NP_065073			brefeldin A-inhibited guanine						regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity			ovary(1)|skin(1)	2	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)														---	---	---	---
KIAA1244	57221	broad.mit.edu	37	6	138640256	138640261	+	Intron	DEL	TTTTTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138640256_138640261delTTTTTT	uc003qhu.2	+							NM_020340	NP_065073			brefeldin A-inhibited guanine						regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity			ovary(1)|skin(1)	2	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	138974698	138974698	+	IGR	DEL	A	-	-	rs79113738		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138974698delA								NHSL1 (81030 upstream) : CCDC28A (119959 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	139094629	139094630	+	Intron	INS	-	G	G	rs143951524	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139094629_139094630insG	uc003qid.1	-						CCDC28A_uc003qie.2_5'Flank					Homo sapiens cDNA FLJ35273 fis, clone PROST2006020.																														---	---	---	---
TXLNB	167838	broad.mit.edu	37	6	139616125	139616126	+	5'Flank	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139616125_139616126insA	uc011eds.1	-							NM_153235	NP_694967			taxilin beta							cytoplasm				large_intestine(1)|ovary(1)	2				OV - Ovarian serous cystadenocarcinoma(155;0.000185)|GBM - Glioblastoma multiforme(68;0.000235)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	139728075	139728075	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139728075delA								CITED2 (32290 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	141150641	141150641	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:141150641delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	141228119	141228119	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:141228119delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	141424470	141424470	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:141424470delT								None (None upstream) : NMBR (972276 downstream)																																			---	---	---	---
LOC153910	153910	broad.mit.edu	37	6	142850759	142850759	+	Intron	DEL	T	-	-	rs71683237		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142850759delT	uc003qjc.1	-						LOC153910_uc010khg.1_Intron	NR_027312				Homo sapiens cDNA FLJ31371 fis, clone NB9N42000196.												0																		---	---	---	---
LOC153910	153910	broad.mit.edu	37	6	142865362	142865362	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142865362delA	uc003qjc.1	-						LOC153910_uc010khg.1_Intron	NR_027312				Homo sapiens cDNA FLJ31371 fis, clone NB9N42000196.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	144564281	144564281	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144564281delT								STX11 (51206 upstream) : UTRN (43209 downstream)																																			---	---	---	---
UTRN	7402	broad.mit.edu	37	6	144750959	144750959	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144750959delT	uc003qkt.2	+						UTRN_uc010khq.1_Intron	NM_007124	NP_009055			utrophin						muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)														---	---	---	---
UTRN	7402	broad.mit.edu	37	6	144806372	144806372	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144806372delT	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	144837921	144837921	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144837921delT	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	145044987	145044987	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145044987delA	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	145093031	145093031	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145093031delT	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	145126769	145126769	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145126769delG	uc003qkt.2	+							NM_007124	NP_009055			utrophin						muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	145794598	145794598	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145794598delG								UTRN (620430 upstream) : EPM2A (151848 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	146301587	146301587	+	IGR	DEL	A	-	-	rs78264533		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146301587delA								SHPRH (16028 upstream) : GRM1 (47195 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	146903469	146903469	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146903469delA								RAB32 (27383 upstream) : C6orf103 (16667 downstream)																																			---	---	---	---
C6orf103	79747	broad.mit.edu	37	6	146917862	146917864	+	5'Flank	DEL	TAT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146917862_146917864delTAT	uc010khx.2	+						C6orf103_uc003qlp.2_5'Flank	NM_024694	NP_078970			hypothetical protein LOC79747						oxygen transport|proteolysis	intracellular	calcium-dependent cysteine-type endopeptidase activity|heme binding|oxygen binding			central_nervous_system(2)|lung(1)	3		Ovarian(120;0.142)		OV - Ovarian serous cystadenocarcinoma(155;2.04e-08)|GBM - Glioblastoma multiforme(68;0.0113)														---	---	---	---
C6orf103	79747	broad.mit.edu	37	6	147045247	147045247	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147045247delA	uc010khx.2	+						C6orf103_uc003qlp.2_Intron|C6orf103_uc003qlq.2_Intron	NM_024694	NP_078970			hypothetical protein LOC79747						oxygen transport|proteolysis	intracellular	calcium-dependent cysteine-type endopeptidase activity|heme binding|oxygen binding			central_nervous_system(2)|lung(1)	3		Ovarian(120;0.142)		OV - Ovarian serous cystadenocarcinoma(155;2.04e-08)|GBM - Glioblastoma multiforme(68;0.0113)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	147909806	147909806	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147909806delT								SAMD5 (18649 upstream) : SASH1 (753923 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	148148454	148148454	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148148454delA								SAMD5 (257297 upstream) : SASH1 (515275 downstream)																																			---	---	---	---
SASH1	23328	broad.mit.edu	37	6	148729172	148729172	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148729172delT	uc003qme.1	+							NM_015278	NP_056093			SAM and SH3 domain containing 1								protein binding			central_nervous_system(1)	1		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	148890280	148890280	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148890280delA								SASH1 (17096 upstream) : UST (177991 downstream)																																			---	---	---	---
UST	10090	broad.mit.edu	37	6	149244259	149244259	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149244259delA	uc003qmg.2	+							NM_005715	NP_005706			uronyl-2-sulfotransferase						protein sulfation	Golgi membrane|integral to membrane	sulfotransferase activity			ovary(2)	2		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.78e-10)|GBM - Glioblastoma multiforme(68;0.138)														---	---	---	---
LRP11	84918	broad.mit.edu	37	6	150147575	150147575	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150147575delT	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)														---	---	---	---
ESR1	2099	broad.mit.edu	37	6	152163717	152163717	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152163717delT	uc003qom.3	+						ESR1_uc010kin.2_Intron|ESR1_uc010kio.2_Intron|ESR1_uc010kip.2_Intron|ESR1_uc003qon.3_Intron|ESR1_uc003qoo.3_Intron|ESR1_uc010kiq.2_Intron|ESR1_uc010kir.2_Intron|ESR1_uc011eet.1_5'Flank|ESR1_uc011eeu.1_5'Flank|ESR1_uc011eev.1_5'Flank|ESR1_uc011eew.1_5'Flank	NM_001122742	NP_001116214			estrogen receptor alpha isoform 4						positive regulation of retinoic acid receptor signaling pathway|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to estradiol stimulus	chromatin remodeling complex|cytoplasm|nucleoplasm	beta-catenin binding|enzyme binding|estrogen receptor activity|estrogen response element binding|nitric-oxide synthase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding			central_nervous_system(2)|ovary(1)|lung(1)|breast(1)	5		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Chlorotrianisene(DB00269)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Dromostanolone(DB00858)|Drospirenone(DB01395)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Letrozole(DB01006)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)													---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152783719	152783720	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152783719_152783720insT	uc010kiw.2	-						SYNE1_uc003qot.3_Intron|SYNE1_uc003qou.3_Intron|SYNE1_uc010kjb.1_Intron|SYNE1_uc003qpa.1_3'UTR|SYNE1_uc003qow.2_Intron|SYNE1_uc003qox.1_Intron|SYNE1_uc003qoz.2_Intron|SYNE1_uc003qoy.2_Intron	NM_182961	NP_892006			spectrin repeat containing, nuclear envelope 1						cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)											HNSCC(10;0.0054)			---	---	---	---
RGS17	26575	broad.mit.edu	37	6	153367356	153367357	+	Intron	INS	-	T	T	rs142438828	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153367356_153367357insT	uc003qpm.2	-							NM_012419	NP_036551			regulator of G-protein signalling 17						negative regulation of signal transduction	cytoplasm|nucleus|plasma membrane	GTPase activator activity|signal transducer activity			pancreas(1)	1		Ovarian(120;0.126)		OV - Ovarian serous cystadenocarcinoma(155;1.09e-09)|BRCA - Breast invasive adenocarcinoma(81;0.0429)										Lung_Cancer_Familial_Clustering_of				---	---	---	---
RGS17	26575	broad.mit.edu	37	6	153391358	153391358	+	Intron	DEL	C	-	-	rs1933263	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153391358delC	uc003qpm.2	-							NM_012419	NP_036551			regulator of G-protein signalling 17						negative regulation of signal transduction	cytoplasm|nucleus|plasma membrane	GTPase activator activity|signal transducer activity			pancreas(1)	1		Ovarian(120;0.126)		OV - Ovarian serous cystadenocarcinoma(155;1.09e-09)|BRCA - Breast invasive adenocarcinoma(81;0.0429)										Lung_Cancer_Familial_Clustering_of				---	---	---	---
Unknown	0	broad.mit.edu	37	6	153469781	153469782	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153469781_153469782insA								RGS17 (17392 upstream) : OPRM1 (861854 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	153631510	153631510	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153631510delA								RGS17 (179121 upstream) : OPRM1 (700126 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	153631736	153631737	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153631736_153631737insA								RGS17 (179347 upstream) : OPRM1 (699899 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	154259550	154259550	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154259550delT								RGS17 (807161 upstream) : OPRM1 (72086 downstream)																																			---	---	---	---
TIAM2	26230	broad.mit.edu	37	6	155178170	155178171	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155178170_155178171delTT	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	156204940	156204940	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156204940delA								NOX3 (427903 upstream) : MIR1202 (62991 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	156321253	156321253	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156321253delA								MIR1202 (53240 upstream) : ARID1B (777833 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	156482078	156482078	+	IGR	DEL	A	-	-	rs66517971		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156482078delA								MIR1202 (214065 upstream) : ARID1B (617008 downstream)																																			---	---	---	---
ARID1B	57492	broad.mit.edu	37	6	157383339	157383340	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157383339_157383340delTT	uc003qqn.2	+						ARID1B_uc003qqo.2_Intron|ARID1B_uc003qqp.2_Intron|ARID1B_uc003qqq.1_Intron	NM_017519	NP_059989			AT rich interactive domain 1B (SWI1-like)						chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent	SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)|breast(1)	2		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)														---	---	---	---
ARID1B	57492	broad.mit.edu	37	6	157529244	157529244	+	3'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157529244delT	uc003qqn.2	+	20					ARID1B_uc003qqo.2_3'UTR|ARID1B_uc003qqp.2_3'UTR	NM_017519	NP_059989			AT rich interactive domain 1B (SWI1-like)						chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent	SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)|breast(1)	2		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)														---	---	---	---
ZDHHC14	79683	broad.mit.edu	37	6	157901305	157901305	+	Intron	DEL	G	-	-	rs66727828		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157901305delG	uc003qqt.2	+						ZDHHC14_uc003qqs.2_Intron	NM_024630	NP_078906			zinc finger, DHHC-type containing 14 isoform 1							integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)|skin(1)	2		Breast(66;0.00586)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.9e-17)|BRCA - Breast invasive adenocarcinoma(81;5.8e-05)														---	---	---	---
ZDHHC14	79683	broad.mit.edu	37	6	157927974	157927974	+	Intron	DEL	T	-	-	rs67517993		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157927974delT	uc003qqt.2	+						ZDHHC14_uc003qqs.2_Intron	NM_024630	NP_078906			zinc finger, DHHC-type containing 14 isoform 1							integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)|skin(1)	2		Breast(66;0.00586)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.9e-17)|BRCA - Breast invasive adenocarcinoma(81;5.8e-05)														---	---	---	---
TULP4	56995	broad.mit.edu	37	6	158900957	158900957	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158900957delC	uc003qrf.2	+	7	2558	c.1201delC	c.(1201-1203)CCCfs	p.P401fs	TULP4_uc011efo.1_Frame_Shift_Del_p.P401fs|TULP4_uc003qrg.2_Frame_Shift_Del_p.P401fs	NM_020245	NP_064630	Q9NRJ4	TULP4_HUMAN	tubby like protein 4 isoform 1	401	SOCS box.				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	158932014	158932014	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158932014delA	uc003qrf.2	+	14					TULP4_uc003qrg.2_3'UTR	NM_020245	NP_064630			tubby like protein 4 isoform 1						intracellular signal transduction|response to nutrient	cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	159534510	159534511	+	IGR	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159534510_159534511delGT								TAGAP (68326 upstream) : FNDC1 (55918 downstream)																																			---	---	---	---
WTAP	9589	broad.mit.edu	37	6	160162983	160162983	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160162983delA	uc003qsl.2	+						WTAP_uc010kjx.2_Intron|WTAP_uc003qsk.2_Intron|WTAP_uc003qsm.1_Intron|WTAP_uc003qsn.2_Intron	NM_004906	NP_004897			Wilms' tumour 1-associating protein isoform 1						cell cycle|mRNA processing|RNA splicing	nuclear membrane|nucleolus					0		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.75e-18)|BRCA - Breast invasive adenocarcinoma(81;5.93e-06)														---	---	---	---
ACAT2	39	broad.mit.edu	37	6	160198777	160198778	+	Intron	DEL	TA	-	-	rs143069477		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160198777_160198778delTA	uc010kjy.2	+						ACAT2_uc011efw.1_Intron	NM_005891	NP_005882			acetyl-Coenzyme A acetyltransferase 2							mitochondrion|nucleolus	acetyl-CoA C-acetyltransferase activity|protein binding			ovary(1)|central_nervous_system(1)	2		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.51e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)														---	---	---	---
IGF2R	3482	broad.mit.edu	37	6	160439786	160439786	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160439786delA	uc003qta.2	+							NM_000876	NP_000867			insulin-like growth factor 2 receptor precursor						receptor-mediated endocytosis	cell surface|endocytic vesicle|endosome|integral to plasma membrane|lysosomal membrane|trans-Golgi network transport vesicle	glycoprotein binding|insulin-like growth factor receptor activity|phosphoprotein binding|transporter activity			ovary(3)	3		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)														---	---	---	---
MAP3K4	4216	broad.mit.edu	37	6	161491963	161491963	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161491963delT	uc003qtn.2	+						MAP3K4_uc010kkc.1_Intron|MAP3K4_uc003qto.2_Intron|MAP3K4_uc011efz.1_Intron|MAP3K4_uc011ega.1_Intron	NM_005922	NP_005913			mitogen-activated protein kinase kinase kinase 4						activation of MAPKK activity|JNK cascade|positive regulation of JUN kinase activity	perinuclear region of cytoplasm	ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein binding			ovary(3)|lung(3)|skin(2)|stomach(1)	9		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)														---	---	---	---
PARK2	5071	broad.mit.edu	37	6	161807728	161807728	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161807728delT	uc003qtx.3	-						PARK2_uc003qtv.3_Intron|PARK2_uc010kkd.2_Intron|PARK2_uc003qtw.3_Intron|PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc011egf.1_Intron	NM_004562	NP_004553			parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)														---	---	---	---
PARK2	5071	broad.mit.edu	37	6	162027987	162027988	+	Intron	INS	-	G	G	rs71802397		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162027987_162027988insG	uc003qtx.3	-						PARK2_uc003qtv.3_Intron|PARK2_uc010kkd.2_Intron|PARK2_uc003qtw.3_Intron|PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron|PARK2_uc011egf.1_Intron	NM_004562	NP_004553			parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)														---	---	---	---
PARK2	5071	broad.mit.edu	37	6	162083933	162083933	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162083933delC	uc003qtx.3	-						PARK2_uc003qtv.3_Intron|PARK2_uc010kkd.2_Intron|PARK2_uc003qtw.3_Intron|PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron|PARK2_uc011egf.1_Intron	NM_004562	NP_004553			parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)														---	---	---	---
PARK2	5071	broad.mit.edu	37	6	162813179	162813179	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162813179delA	uc003qtx.3	-						PARK2_uc010kkd.2_Intron|PARK2_uc003qtw.3_Intron|PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron	NM_004562	NP_004553			parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)														---	---	---	---
PACRG	135138	broad.mit.edu	37	6	163420130	163420130	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163420130delA	uc003qua.2	+						PACRG_uc003qub.2_Intron|PACRG_uc003quc.2_Intron	NM_152410	NP_689623			parkin co-regulated gene protein isoform 1												0		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	163824144	163824145	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163824144_163824145delTT								LOC285796 (78650 upstream) : QKI (11530 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	164035966	164035966	+	IGR	DEL	A	-	-	rs11302380		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164035966delA								QKI (41074 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	164900172	164900172	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164900172delA								QKI (905280 upstream) : C6orf118 (792983 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	165245215	165245215	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165245215delT								None (None upstream) : C6orf118 (447940 downstream)																																			---	---	---	---
PDE10A	10846	broad.mit.edu	37	6	166004597	166004597	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166004597delA	uc003qun.2	-						PDE10A_uc003quo.2_Intron	NM_006661	NP_006652			phosphodiesterase 10A isoform 2						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cAMP binding|cGMP binding|metal ion binding			ovary(3)|skin(2)	5		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Dipyridamole(DB00975)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	166176424	166176425	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166176424_166176425delAA								PDE10A (100840 upstream) : C6orf176 (161111 downstream)																																			---	---	---	---
C6orf176	90632	broad.mit.edu	37	6	166384628	166384628	+	Intron	DEL	A	-	-	rs66602976		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166384628delA	uc011egl.1	-						uc003qup.1_Intron|C6orf176_uc003quq.3_Intron|C6orf176_uc003qur.2_Intron	NR_026861				Homo sapiens cDNA FLJ76352 complete cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	166505402	166505402	+	IGR	DEL	T	-	-	rs67413350		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166505402delT								LOC441177 (102299 upstream) : T (65684 downstream)																																			---	---	---	---
RPS6KA2	6196	broad.mit.edu	37	6	167073909	167073910	+	Intron	INS	-	GA	GA	rs148446807	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167073909_167073910insGA	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	168052583	168052584	+	IGR	INS	-	TA	TA			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168052583_168052584insTA								TCP10 (254585 upstream) : C6orf123 (132637 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	168087718	168087719	+	Intron	DEL	TG	-	-	rs141067302		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168087718_168087719delTG	uc003qvy.1	-											Homo sapiens cDNA FLJ32038 fis, clone NTONG2000583.																														---	---	---	---
KIF25	3834	broad.mit.edu	37	6	168420143	168420143	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168420143delA	uc003qwk.1	+						KIF25_uc010kkt.1_Intron|KIF25_uc003qwl.1_Intron	NM_030615	NP_085118			kinesin family member 25 isoform 1						microtubule-based movement|mitotic sister chromatid segregation	cytoplasm|kinesin complex|microtubule	ATP binding|microtubule motor activity			ovary(1)|pancreas(1)	2		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)														---	---	---	---
SMOC2	64094	broad.mit.edu	37	6	169059551	169059552	+	Intron	INS	-	TG	TG	rs148960064	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169059551_169059552insTG	uc003qws.1	+						SMOC2_uc003qwr.1_Intron|SMOC2_uc011egu.1_Intron	NM_022138	NP_071421			SPARC related modular calcium binding 2						signal transduction	basement membrane	calcium ion binding			ovary(1)	1		Breast(66;0.000141)|Esophageal squamous(34;0.222)|Ovarian(120;0.231)		OV - Ovarian serous cystadenocarcinoma(33;1.31e-19)|BRCA - Breast invasive adenocarcinoma(81;3.06e-06)|GBM - Glioblastoma multiforme(31;0.00109)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	169240574	169240574	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169240574delG								SMOC2 (171903 upstream) : THBS2 (375302 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	169519345	169519348	+	IGR	DEL	AAAA	-	-	rs74360901		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169519345_169519348delAAAA								SMOC2 (450674 upstream) : THBS2 (96528 downstream)																																			---	---	---	---
THBS2	7058	broad.mit.edu	37	6	169619451	169619458	+	Intron	DEL	TTGGGTGA	-	-	rs116989814	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169619451_169619458delTTGGGTGA	uc003qwt.2	-							NM_003247	NP_003238			thrombospondin 2 precursor						cell adhesion	extracellular region	calcium ion binding|heparin binding|protein binding|structural molecule activity			ovary(5)	5		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)														---	---	---	---
WDR27	253769	broad.mit.edu	37	6	169878058	169878058	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169878058delA	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)														---	---	---	---
PHF10	55274	broad.mit.edu	37	6	170118766	170118766	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170118766delA	uc011egy.1	-						PHF10_uc011egz.1_Intron|PHF10_uc011eha.1_5'Flank	NM_018288	NP_060758			PHD finger protein 10 isoform a						nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	npBAF complex	zinc ion binding			urinary_tract(1)	1		Breast(66;5.08e-05)|Ovarian(120;0.208)		OV - Ovarian serous cystadenocarcinoma(33;1.4e-21)|BRCA - Breast invasive adenocarcinoma(81;1.4e-07)|GBM - Glioblastoma multiforme(31;0.00176)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	170611348	170611348	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170611348delA								DLL1 (11651 upstream) : FAM120B (4496 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	834184	834185	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:834184_834185delTT								HEATR2 (8068 upstream) : SUN1 (22067 downstream)																																			---	---	---	---
ADAP1	11033	broad.mit.edu	37	7	945510	945510	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:945510delG	uc003sjo.3	-						ADAP1_uc003sjm.3_5'Flank|ADAP1_uc011jvs.1_Intron|ADAP1_uc003sjn.3_Intron|ADAP1_uc010ksc.2_Intron	NM_006869	NP_006860			centaurin, alpha 1						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																		---	---	---	---
ADAP1	11033	broad.mit.edu	37	7	945716	945717	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:945716_945717insA	uc003sjo.3	-						ADAP1_uc003sjm.3_5'Flank|ADAP1_uc011jvs.1_Intron|ADAP1_uc003sjn.3_Intron|ADAP1_uc010ksc.2_Intron	NM_006869	NP_006860			centaurin, alpha 1						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																		---	---	---	---
ADAP1	11033	broad.mit.edu	37	7	945717	945718	+	Intron	INS	-	AGA	AGA			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:945717_945718insAGA	uc003sjo.3	-						ADAP1_uc003sjm.3_5'Flank|ADAP1_uc011jvs.1_Intron|ADAP1_uc003sjn.3_Intron|ADAP1_uc010ksc.2_Intron	NM_006869	NP_006860			centaurin, alpha 1						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	1382994	1382994	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1382994delA								UNCX (106382 upstream) : MICALL2 (91002 downstream)																																			---	---	---	---
TTYH3	80727	broad.mit.edu	37	7	2690347	2690347	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2690347delG	uc003smp.2	+						TTYH3_uc010ksn.2_Intron|TTYH3_uc003smq.2_Intron	NM_025250	NP_079526			tweety 3							chloride channel complex|plasma membrane	chloride channel activity				0		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.04e-14)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	2932165	2932165	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2932165delA								GNA12 (48206 upstream) : CARD11 (13604 downstream)																																			---	---	---	---
CARD11	84433	broad.mit.edu	37	7	3083504	3083504	+	5'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3083504delA	uc003smv.2	-	1						NM_032415	NP_115791			caspase recruitment domain family, member 11						positive regulation of cytokine production|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis|T cell costimulation|T cell receptor signaling pathway	cytosol|membrane raft|plasma membrane	CARD domain binding|guanylate kinase activity			haematopoietic_and_lymphoid_tissue(43)|ovary(2)|kidney(2)|skin(2)|central_nervous_system(1)	50		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)				Mis		DLBCL								---	---	---	---
SDK1	221935	broad.mit.edu	37	7	3463204	3463205	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3463204_3463205insT	uc003smx.2	+							NM_152744	NP_689957			sidekick 1 precursor						cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	4549098	4549098	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4549098delA								SDK1 (240469 upstream) : FOXK1 (134290 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	4571531	4571531	+	IGR	DEL	G	-	-	rs112594851		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4571531delG								SDK1 (262902 upstream) : FOXK1 (111857 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	5282486	5282497	+	IGR	DEL	AAGCAAGCAAGC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5282486_5282497delAAGCAAGCAAGC								WIPI2 (9001 upstream) : SLC29A4 (40064 downstream)																																			---	---	---	---
TNRC18	84629	broad.mit.edu	37	7	5371093	5371093	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5371093delA	uc003soi.3	-							NM_001080495	NP_001073964			trinucleotide repeat containing 18								DNA binding				0		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	5623034	5623034	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5623034delA								ACTB (52802 upstream) : FSCN1 (9420 downstream)																																			---	---	---	---
PMS2	5395	broad.mit.edu	37	7	6036896	6036896	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6036896delA	uc003spl.2	-						PMS2_uc003spj.2_Intron|PMS2_uc003spk.2_Intron|PMS2_uc011jwl.1_Intron|PMS2_uc010ktg.2_Intron|PMS2_uc010kte.2_Intron|PMS2_uc010ktf.1_Intron	NM_000535	NP_000526			PMS2 postmeiotic segregation increased 2 isoform						mismatch repair|reciprocal meiotic recombination|somatic hypermutation of immunoglobulin genes	MutLalpha complex	ATP binding|ATPase activity|endonuclease activity|protein binding|single base insertion or deletion binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)				Mis|N|F			colorectal|endometrial|ovarian|medulloblastoma|glioma		Direct_reversal_of_damage|MMR	Lynch_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	7	6402254	6402254	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6402254delA								C7orf70 (13664 upstream) : RAC1 (11872 downstream)																																			---	---	---	---
C7orf28B	221960	broad.mit.edu	37	7	6862164	6862165	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6862164_6862165insA	uc003sqx.1	-						C7orf28B_uc011jxd.1_Intron	NM_198097	NP_932765			hypothetical protein LOC221960							lysosomal membrane					0		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.175)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	7094406	7094406	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7094406delA								C7orf28B (228545 upstream) : C1GALT1 (127840 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	7926665	7926665	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7926665delT								RPA3 (168427 upstream) : GLCCI1 (81758 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	9074156	9074156	+	IGR	DEL	T	-	-	rs35472333		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:9074156delT								NXPH1 (281564 upstream) : PER4 (599744 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	9562620	9562621	+	IGR	DEL	TG	-	-	rs34742433		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:9562620_9562621delTG								NXPH1 (770028 upstream) : PER4 (111279 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	9975063	9975063	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:9975063delT								PER4 (299616 upstream) : NDUFA4 (997752 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	10623529	10623529	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10623529delT								PER4 (948082 upstream) : NDUFA4 (349286 downstream)																																			---	---	---	---
NDUFA4	4697	broad.mit.edu	37	7	10978274	10978274	+	Intron	DEL	A	-	-	rs10272132	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10978274delA	uc003srx.1	-							NM_002489	NP_002480			NADH dehydrogenase (ubiquinone) 1 alpha						mitochondrial electron transport, NADH to ubiquinone|transport	mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity				0				UCEC - Uterine corpus endometrioid carcinoma (126;0.177)	NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	11369183	11369186	+	Intron	DEL	TGCG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11369183_11369186delTGCG	uc003ssb.2	+											Homo sapiens cDNA clone IMAGE:4830466.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	11369190	11369193	+	Intron	DEL	GTGT	-	-	rs57248036	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11369190_11369193delGTGT	uc003ssb.2	+											Homo sapiens cDNA clone IMAGE:4830466.																														---	---	---	---
THSD7A	221981	broad.mit.edu	37	7	11441208	11441208	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11441208delT	uc003ssf.3	-							NM_015204	NP_056019			thrombospondin, type I, domain containing 7A							integral to membrane				ovary(3)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)											HNSCC(18;0.044)			---	---	---	---
THSD7A	221981	broad.mit.edu	37	7	11540572	11540573	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11540572_11540573insA	uc003ssf.3	-							NM_015204	NP_056019			thrombospondin, type I, domain containing 7A							integral to membrane				ovary(3)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)											HNSCC(18;0.044)			---	---	---	---
Unknown	0	broad.mit.edu	37	7	12451549	12451550	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12451549_12451550delAA								VWDE (7697 upstream) : SCIN (144637 downstream)																																			---	---	---	---
SCIN	85477	broad.mit.edu	37	7	12655052	12655053	+	Intron	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12655052_12655053delCT	uc003ssn.3	+						SCIN_uc010ktt.2_Intron|SCIN_uc003sso.3_Intron	NM_001112706	NP_001106177			scinderin isoform 1						actin filament capping|actin filament severing|actin nucleation|calcium ion-dependent exocytosis|negative regulation of cell proliferation|positive regulation of apoptosis|positive regulation of megakaryocyte differentiation|positive regulation of secretion|regulation of chondrocyte differentiation	cell cortex|cytoskeleton	1-phosphatidylinositol binding|actin filament binding|calcium ion binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylserine binding			ovary(2)	2				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)														---	---	---	---
SCIN	85477	broad.mit.edu	37	7	12658723	12658723	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12658723delG	uc003ssn.3	+						SCIN_uc010ktt.2_Intron|SCIN_uc003sso.3_Intron	NM_001112706	NP_001106177			scinderin isoform 1						actin filament capping|actin filament severing|actin nucleation|calcium ion-dependent exocytosis|negative regulation of cell proliferation|positive regulation of apoptosis|positive regulation of megakaryocyte differentiation|positive regulation of secretion|regulation of chondrocyte differentiation	cell cortex|cytoskeleton	1-phosphatidylinositol binding|actin filament binding|calcium ion binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylserine binding			ovary(2)	2				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	13029898	13029899	+	IGR	DEL	CA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:13029898_13029899delCA								ARL4A (299342 upstream) : ETV1 (900959 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	13298745	13298748	+	IGR	DEL	TTTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:13298745_13298748delTTTT								ARL4A (568189 upstream) : ETV1 (632110 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	13541973	13541973	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:13541973delA								ARL4A (811417 upstream) : ETV1 (388885 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	13582303	13582303	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:13582303delA								ARL4A (851747 upstream) : ETV1 (348555 downstream)																																			---	---	---	---
DGKB	1607	broad.mit.edu	37	7	14925112	14925112	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:14925112delA	uc011jxt.1	-						DGKB_uc011jxv.1_Intron	NM_004080	NP_004071			diacylglycerol kinase, beta isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity|protein binding			lung(5)|ovary(4)|breast(2)|skin(1)	12					Phosphatidylserine(DB00144)													---	---	---	---
TMEM195	392636	broad.mit.edu	37	7	15249018	15249019	+	Intron	DEL	GT	-	-	rs36035537		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15249018_15249019delGT	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	15542730	15542730	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15542730delT	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	15557660	15557660	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15557660delA	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	15613597	15613597	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15613597delT								TMEM195 (11957 upstream) : MEOX2 (37242 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	16022334	16022335	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16022334_16022335delAC								MEOX2 (296026 upstream) : ISPD (104817 downstream)																																			---	---	---	---
ISPD	729920	broad.mit.edu	37	7	16156329	16156330	+	Intron	DEL	GA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16156329_16156330delGA	uc010ktx.2	-						ISPD_uc010kty.2_Intron	NM_001101426	NP_001094896			notch1-induced protein isoform a						isoprenoid biosynthetic process		nucleotidyltransferase activity			ovary(1)	1															Multiple Myeloma(15;0.18)			---	---	---	---
ISPD	729920	broad.mit.edu	37	7	16329980	16329980	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16329980delA	uc010ktx.2	-						ISPD_uc010kty.2_Intron	NM_001101426	NP_001094896			notch1-induced protein isoform a						isoprenoid biosynthetic process		nucleotidyltransferase activity			ovary(1)	1															Multiple Myeloma(15;0.18)			---	---	---	---
Unknown	0	broad.mit.edu	37	7	16467969	16467970	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16467969_16467970delTG								ISPD (7022 upstream) : SOSTDC1 (33138 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	16495121	16495121	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16495121delA								ISPD (34174 upstream) : SOSTDC1 (5987 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	16620978	16620978	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16620978delT								SOSTDC1 (50773 upstream) : ANKMY2 (18435 downstream)																																			---	---	---	---
HDAC9	9734	broad.mit.edu	37	7	18178151	18178152	+	Intron	DEL	GT	-	-	rs72289605		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18178151_18178152delGT	uc011jya.1	+							NM_014707	NP_055522			histone deacetylase 9 isoform 3						B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein binding|protein kinase C binding|repressing transcription factor binding|transcription corepressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)													---	---	---	---
HDAC9	9734	broad.mit.edu	37	7	18424393	18424395	+	Intron	DEL	AAA	-	-	rs111871459		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18424393_18424395delAAA	uc003sua.1	+						HDAC9_uc011jya.1_Intron	NM_014707	NP_055522			histone deacetylase 9 isoform 3						B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein binding|protein kinase C binding|repressing transcription factor binding|transcription corepressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)													---	---	---	---
HDAC9	9734	broad.mit.edu	37	7	19006341	19006341	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:19006341delA	uc003sui.2	+						HDAC9_uc003sue.2_Intron|HDAC9_uc003suj.2_Intron|HDAC9_uc003suk.2_Intron	NM_178425	NP_848512			histone deacetylase 9 isoform 5						B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein binding|protein kinase C binding|repressing transcription factor binding|transcription corepressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	20097640	20097641	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20097640_20097641delAC								TMEM196 (284424 upstream) : MACC1 (76647 downstream)																																			---	---	---	---
MACC1	346389	broad.mit.edu	37	7	20229416	20229417	+	Intron	INS	-	AG	AG			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20229416_20229417insAG	uc003sus.3	-						MACC1_uc010kug.2_Intron	NM_182762	NP_877439			putative binding protein 7a5						positive regulation of cell division|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	growth factor activity			ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	20281063	20281063	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20281063delT								MACC1 (24050 upstream) : ITGB8 (89262 downstream)																																			---	---	---	---
SP8	221833	broad.mit.edu	37	7	20826480	20826480	+	5'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20826480delT	uc003suy.2	-	1					SP8_uc003suz.2_5'UTR	NM_198956	NP_945194			Sp8 transcription factor isoform 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	21451207	21451207	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21451207delT								RPL23P8 (583768 upstream) : SP4 (16482 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	21565737	21565737	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21565737delA								SP4 (11588 upstream) : DNAH11 (17096 downstream)																																			---	---	---	---
DNAH11	8701	broad.mit.edu	37	7	21870299	21870300	+	Intron	INS	-	A	A	rs145857793	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21870299_21870300insA	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	22017434	22017434	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22017434delA								CDCA7L (31892 upstream) : RAPGEF5 (140475 downstream)																																			---	---	---	---
RAPGEF5	9771	broad.mit.edu	37	7	22185586	22185587	+	Intron	DEL	GT	-	-	rs71864981		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22185586_22185587delGT	uc003svg.2	-						RAPGEF5_uc011jyl.1_Intron	NM_012294	NP_036426			Rap guanine nucleotide exchange factor (GEF) 5						nervous system development|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	nucleus	GTP-dependent protein binding|Rap guanyl-nucleotide exchange factor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	22433501	22433501	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22433501delG								RAPGEF5 (36968 upstream) : MGC87042 (25565 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	22903497	22903497	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22903497delA								SNORD93 (7193 upstream) : FAM126A (77390 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	22936248	22936248	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22936248delA								SNORD93 (39944 upstream) : FAM126A (44639 downstream)																																			---	---	---	---
FAM126A	84668	broad.mit.edu	37	7	23000682	23000682	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23000682delA	uc003svm.3	-						FAM126A_uc003svn.3_Intron	NM_032581	NP_115970			family with sequence similarity 126, member A							cytoplasm|membrane	signal transducer activity			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	23125503	23125504	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23125503_23125504delAA								FAM126A (71733 upstream) : KLHL7 (19849 downstream)																																			---	---	---	---
NUPL2	11097	broad.mit.edu	37	7	23239759	23239759	+	Intron	DEL	T	-	-	rs112626242		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23239759delT	uc003svu.2	+						NUPL2_uc003svv.2_Intron|NUPL2_uc003svw.2_Intron|NUPL2_uc011jyw.1_Intron|NUPL2_uc003svx.2_Intron|NUPL2_uc011jyx.1_Intron	NM_007342	NP_031368			nucleoporin like 2						carbohydrate metabolic process|glucose transport|mRNA transport|protein export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear membrane|nuclear pore	nuclear export signal receptor activity|nucleic acid binding|zinc ion binding			skin(2)|ovary(1)	3																		---	---	---	---
C7orf30	115416	broad.mit.edu	37	7	23347411	23347411	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23347411delA	uc003swd.1	+						C7orf30_uc003swe.2_5'Flank	NM_138446	NP_612455			hypothetical protein LOC115416							mitochondrion					0			GBM - Glioblastoma multiforme(13;0.154)															---	---	---	---
IGF2BP3	10643	broad.mit.edu	37	7	23417978	23417978	+	Intron	DEL	A	-	-	rs35304098		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23417978delA	uc003swg.2	-							NM_006547	NP_006538			insulin-like growth factor 2 mRNA binding						anatomical structure morphogenesis|negative regulation of translation|translation	cytosol|nucleus	mRNA 3'-UTR binding|mRNA 5'-UTR binding|nucleotide binding|protein binding|translation regulator activity			ovary(2)	2																		---	---	---	---
IGF2BP3	10643	broad.mit.edu	37	7	23436325	23436325	+	Intron	DEL	A	-	-	rs12700427	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23436325delA	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																		---	---	---	---
C7orf46	340277	broad.mit.edu	37	7	23724876	23724885	+	Intron	DEL	CAAAACAAAA	-	-	rs71824329		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23724876_23724885delCAAAACAAAA	uc003swo.3	+						C7orf46_uc003swq.3_Intron|C7orf46_uc003swr.3_Intron|C7orf46_uc003swp.3_Intron|C7orf46_uc010kup.2_Intron	NM_199136	NP_954587			hypothetical protein LOC340277 isoform 1												0																		---	---	---	---
STK31	56164	broad.mit.edu	37	7	23788964	23788965	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23788964_23788965delTT	uc003sws.3	+						STK31_uc003swt.3_Intron|STK31_uc011jze.1_Intron|STK31_uc010kuq.2_Intron	NM_031414	NP_113602			serine/threonine kinase 31 isoform a								ATP binding|nucleic acid binding|protein serine/threonine kinase activity			skin(3)|lung(2)|ovary(2)|stomach(2)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	24551663	24551663	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24551663delA								NPY (220186 upstream) : MPP6 (61422 downstream)																																			---	---	---	---
OSBPL3	26031	broad.mit.edu	37	7	24914292	24914292	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24914292delT	uc003sxf.2	-						OSBPL3_uc003sxd.2_Intron|OSBPL3_uc003sxe.2_Intron|OSBPL3_uc003sxg.2_Intron|OSBPL3_uc003sxh.2_Intron|OSBPL3_uc003sxi.2_Intron	NM_015550	NP_056365			oxysterol-binding protein-like protein 3 isoform						lipid transport		lipid binding|protein binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	25174010	25174010	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25174010delA								CYCS (9055 upstream) : C7orf31 (306 downstream)																																			---	---	---	---
LOC441204	441204	broad.mit.edu	37	7	26473516	26473518	+	Intron	DEL	CTC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26473516_26473518delCTC	uc003sxy.1	+						LOC441204_uc003sxz.2_Intron					Homo sapiens cDNA FLJ31922 fis, clone NT2RP7005219.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	26602620	26602620	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26602620delC								KIAA0087 (24176 upstream) : C7orf71 (74870 downstream)																																			---	---	---	---
SKAP2	8935	broad.mit.edu	37	7	26731812	26731813	+	Intron	INS	-	G	G	rs146413662	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26731812_26731813insG	uc003syc.2	-						SKAP2_uc011jzi.1_Intron|SKAP2_uc011jzj.1_Intron	NM_003930	NP_003921			src kinase associated phosphoprotein 2						B cell activation|cell junction assembly|protein complex assembly|signal transduction	cytosol|plasma membrane	SH3/SH2 adaptor activity			pancreas(1)	1																		---	---	---	---
SKAP2	8935	broad.mit.edu	37	7	26838902	26838902	+	Intron	DEL	A	-	-	rs149691668		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26838902delA	uc003syc.2	-						SKAP2_uc011jzi.1_Intron|SKAP2_uc011jzj.1_Intron	NM_003930	NP_003921			src kinase associated phosphoprotein 2						B cell activation|cell junction assembly|protein complex assembly|signal transduction	cytosol|plasma membrane	SH3/SH2 adaptor activity			pancreas(1)	1																		---	---	---	---
TAX1BP1	8887	broad.mit.edu	37	7	27816423	27816423	+	Intron	DEL	T	-	-	rs79417798		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27816423delT	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)															---	---	---	---
TAX1BP1	8887	broad.mit.edu	37	7	27816442	27816442	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27816442delT	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)															---	---	---	---
TAX1BP1	8887	broad.mit.edu	37	7	27868664	27868664	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27868664delA	uc003szl.2	+	17					TAX1BP1_uc011jzo.1_3'UTR|TAX1BP1_uc003szk.2_3'UTR|TAX1BP1_uc011jzp.1_3'UTR	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	28044272	28044272	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28044272delT	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	28726098	28726098	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28726098delA	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	28772944	28772945	+	Intron	INS	-	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28772944_28772945insC	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	28866544	28866544	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28866544delT								CREB5 (1035 upstream) : TRIL (126432 downstream)																																			---	---	---	---
CPVL	54504	broad.mit.edu	37	7	29036166	29036167	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29036166_29036167delAA	uc003szv.2	-						CPVL_uc003szw.2_Intron|CPVL_uc003szx.2_Intron	NM_031311	NP_112601			serine carboxypeptidase vitellogenic-like						proteolysis		protein binding|serine-type carboxypeptidase activity			ovary(2)	2																		---	---	---	---
CPVL	54504	broad.mit.edu	37	7	29111291	29111291	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29111291delA	uc003szv.2	-						CPVL_uc003szw.2_Intron|CPVL_uc003szx.2_Intron	NM_031311	NP_112601			serine carboxypeptidase vitellogenic-like						proteolysis		protein binding|serine-type carboxypeptidase activity			ovary(2)	2																		---	---	---	---
PLEKHA8	84725	broad.mit.edu	37	7	30097681	30097681	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30097681delT	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																		---	---	---	---
PLEKHA8	84725	broad.mit.edu	37	7	30113605	30113607	+	Intron	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30113605_30113607delAAA	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																		---	---	---	---
C7orf41	222166	broad.mit.edu	37	7	30182972	30182972	+	Intron	DEL	T	-	-	rs35968379		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30182972delT	uc011kab.1	+						C7orf41_uc010kvr.1_Intron|C7orf41_uc003tar.1_Intron	NM_152793	NP_690006			hypothetical protein LOC222166												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	30525404	30525404	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30525404delA								NOD1 (7011 upstream) : GGCT (10835 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	30534037	30534037	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30534037delT								NOD1 (15644 upstream) : GGCT (2202 downstream)																																			---	---	---	---
AQP1	358	broad.mit.edu	37	7	30937709	30937712	+	Intron	DEL	TTTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30937709_30937712delTTTT	uc011kac.1	+							NM_198098	NP_932766			aquaporin 1						ammonium transport|cell volume homeostasis|cellular hyperosmotic response|cellular response to cAMP|cellular response to copper ion|cellular response to dexamethasone stimulus|cellular response to hydrogen peroxide|cellular response to hypoxia|cellular response to mechanical stimulus|cellular response to mercury ion|cellular response to nitric oxide|cellular response to retinoic acid|cellular response to salt stress|cellular response to UV|cerebrospinal fluid secretion|cGMP biosynthetic process|establishment or maintenance of actin cytoskeleton polarity|lateral ventricle development|maintenance of symbiont-containing vacuole via substance secreted by host|negative regulation of apoptosis|odontogenesis|pancreatic juice secretion|positive regulation of angiogenesis|positive regulation of fibroblast proliferation|positive regulation of saliva secretion|renal water transport|response to drug|transepithelial water transport	apical plasma membrane|basal plasma membrane|brush border membrane|cytoplasm|integral to plasma membrane|nuclear membrane|sarcolemma|symbiont-containing vacuole	ammonia transmembrane transporter activity|carbon dioxide transmembrane transporter activity|glycerol transmembrane transporter activity|intracellular cGMP activated cation channel activity|nitric oxide transmembrane transporter activity|potassium channel activity|potassium ion transmembrane transporter activity|protein binding|water channel activity				0		Melanoma(862;0.16)			Acetazolamide(DB00819)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	31314070	31314070	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31314070delA								ADCYAP1R1 (167759 upstream) : NEUROD6 (63012 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	31720985	31720988	+	IGR	DEL	GGAT	-	-	rs28633794		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31720985_31720988delGGAT								CCDC129 (22652 upstream) : C7orf16 (5811 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	32459477	32459477	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32459477delC								PDE1C (120536 upstream) : LSM5 (65468 downstream)																																			---	---	---	---
LSM5	23658	broad.mit.edu	37	7	32526806	32526806	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32526806delA	uc003tct.2	-	5					LSM5_uc003tcu.2_RNA|LSM5_uc011kag.1_3'UTR|LSM5_uc011kah.1_3'UTR	NM_012322	NP_036454			LSM5 homolog, U6 small nuclear RNA associated						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|mRNA processing|RNA splicing	cytosol|nucleus|ribonucleoprotein complex	protein binding|RNA binding				0			GBM - Glioblastoma multiforme(11;0.152)															---	---	---	---
AVL9	23080	broad.mit.edu	37	7	32867251	32867251	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32867251delT	uc011kai.1	+						uc003tda.1_Intron	NM_015060	NP_055875			AVL9 homolog (S. cerevisiase)							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	33108969	33108972	+	IGR	DEL	TTTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33108969_33108972delTTTT								NT5C3 (6560 upstream) : RP9 (25440 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	33773771	33773771	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33773771delA								BBS9 (128091 upstream) : BMPER (171341 downstream)																																			---	---	---	---
AAA1	404744	broad.mit.edu	37	7	34445944	34445945	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34445944_34445945delAA	uc010kwo.1	-						AAA1_uc010kwp.1_Intron|AAA1_uc003tdz.2_Intron|AAA1_uc010kwq.1_Intron					Homo sapiens AAA1 variant IA mRNA, complete cds; alternatively spliced.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	34937969	34937969	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34937969delT								NPSR1 (20025 upstream) : DPY19L1 (23112 downstream)																																			---	---	---	---
DPY19L1	23333	broad.mit.edu	37	7	35041774	35041774	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35041774delA	uc003tem.3	-							NM_015283	NP_056098			dpy-19-like 1							integral to membrane					0																		---	---	---	---
TBX20	57057	broad.mit.edu	37	7	35294992	35294992	+	5'Flank	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35294992delA	uc011kas.1	-							NM_001077653	NP_001071121			T-box transcription factor TBX20							nucleus	DNA binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	36063448	36063448	+	IGR	DEL	T	-	-	rs113816455		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36063448delT								SEPT7 (118533 upstream) : EEPD1 (129388 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	36522130	36522130	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36522130delT								ANLN (28732 upstream) : AOAH (30480 downstream)																																			---	---	---	---
ELMO1	9844	broad.mit.edu	37	7	37393199	37393199	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37393199delA	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	37613842	37613842	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37613842delT								ELMO1 (125312 upstream) : GPR141 (166154 downstream)																																			---	---	---	---
TXNDC3	51314	broad.mit.edu	37	7	37887165	37887173	+	5'Flank	DEL	AGGAGATGG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37887165_37887173delAGGAGATGG	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				---	---	---	---
SFRP4	6424	broad.mit.edu	37	7	37955266	37955266	+	Intron	DEL	A	-	-	rs33948098		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37955266delA	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																		---	---	---	---
STARD3NL	83930	broad.mit.edu	37	7	38231903	38231904	+	Intron	INS	-	G	G	rs142180107	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38231903_38231904insG	uc003tfr.2	+						STARD3NL_uc003tfs.2_Intron|STARD3NL_uc003tft.2_Intron	NM_032016	NP_114405			MLN64 N-terminal homolog							integral to membrane|late endosome membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	38419435	38419436	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38419435_38419436insA								TARP (61846 upstream) : AMPH (3871 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	38982075	38982075	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38982075delA								VPS41 (33275 upstream) : POU6F2 (64333 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	39870050	39870052	+	5'Flank	DEL	TTT	-	-	rs67342811		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39870050_39870052delTTT	uc010kxp.2	+											SubName: Full=Similar to sequence-specific single-stranded-DNA-binding protein;																														---	---	---	---
CDK13	8621	broad.mit.edu	37	7	40039231	40039231	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40039231delT	uc003thh.3	+						CDK13_uc003thi.3_Intron|CDK13_uc011kbf.1_Intron	NM_003718	NP_003709			cell division cycle 2-like 5 isoform 1						alternative nuclear mRNA splicing, via spliceosome|hemopoiesis|interspecies interaction between organisms|phosphorylation of RNA polymerase II C-terminal domain|positive regulation of cell proliferation|regulation of mitosis	nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity			lung(2)|skin(2)|ovary(1)	5																		---	---	---	---
CDK13	8621	broad.mit.edu	37	7	40083917	40083918	+	Intron	DEL	TT	-	-	rs76712295		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40083917_40083918delTT	uc003thh.3	+						CDK13_uc003thi.3_Intron|CDK13_uc011kbf.1_Intron	NM_003718	NP_003709			cell division cycle 2-like 5 isoform 1						alternative nuclear mRNA splicing, via spliceosome|hemopoiesis|interspecies interaction between organisms|phosphorylation of RNA polymerase II C-terminal domain|positive regulation of cell proliferation|regulation of mitosis	nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity			lung(2)|skin(2)|ovary(1)	5																		---	---	---	---
C7orf10	79783	broad.mit.edu	37	7	40228031	40228032	+	Intron	INS	-	C	C	rs72318342		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40228031_40228032insC	uc003thn.1	+						C7orf10_uc003thm.1_Intron|C7orf10_uc003tho.1_Intron	NM_024728	NP_079004			dermal papilla derived protein 13								transferase activity			ovary(2)	2																		---	---	---	---
C7orf10	79783	broad.mit.edu	37	7	40654182	40654182	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40654182delT	uc003thn.1	+						C7orf10_uc003thm.1_Intron|C7orf10_uc003tho.1_Intron	NM_024728	NP_079004			dermal papilla derived protein 13								transferase activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	41165519	41165520	+	IGR	INS	-	TA	TA	rs34659228		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41165519_41165520insTA								C7orf10 (265162 upstream) : INHBA (563083 downstream)																																			---	---	---	---
GLI3	2737	broad.mit.edu	37	7	42022986	42022986	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42022986delA	uc011kbh.1	-						GLI3_uc011kbg.1_Intron	NM_000168	NP_000159			GLI-Kruppel family member GLI3						negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of transcription from RNA polymerase II promoter|thymocyte apoptosis	cilium|cytosol|nucleolus	beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(11)|ovary(3)|large_intestine(2)|central_nervous_system(1)|kidney(1)|pancreas(1)	19														Greig_Cephalopolysyndactyly|Pallister-Hall_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	7	42940466	42940466	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42940466delA								GLI3 (663848 upstream) : C7orf25 (8408 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	43148877	43148878	+	IGR	INS	-	TCG	TCG	rs79746306		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43148877_43148878insTCG								MRPL32 (171426 upstream) : HECW1 (3320 downstream)																																			---	---	---	---
HECW1	23072	broad.mit.edu	37	7	43502093	43502093	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43502093delA	uc003tid.1	+						HECW1_uc011kbi.1_Intron	NM_015052	NP_055867			NEDD4-like ubiquitin-protein ligase 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23																		---	---	---	---
STK17A	9263	broad.mit.edu	37	7	43624797	43624798	+	Intron	DEL	AA	-	-	rs79711093		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43624797_43624798delAA	uc003tih.2	+							NM_004760	NP_004751			serine/threonine kinase 17a						apoptosis|induction of apoptosis|intracellular protein kinase cascade	nucleus	ATP binding|protein serine/threonine kinase activity			skin(2)	2																		---	---	---	---
CAMK2B	816	broad.mit.edu	37	7	44294369	44294375	+	Intron	DEL	ACCAACT	-	-	rs111901158		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44294369_44294375delACCAACT	uc003tkq.2	-						CAMK2B_uc003tkp.2_Intron|CAMK2B_uc003tkx.2_Intron|CAMK2B_uc010kyd.2_Intron|CAMK2B_uc003tkr.2_Intron|CAMK2B_uc003tks.2_Intron|CAMK2B_uc003tku.2_Intron|CAMK2B_uc003tkv.2_Intron|CAMK2B_uc003tkt.2_Intron|CAMK2B_uc003tkw.2_Intron|CAMK2B_uc010kyc.2_Intron	NM_001220	NP_001211			calcium/calmodulin-dependent protein kinase II						interferon-gamma-mediated signaling pathway|synaptic transmission	cytosol|endocytic vesicle membrane|nucleoplasm|plasma membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			large_intestine(1)|ovary(1)	2																		---	---	---	---
CAMK2B	816	broad.mit.edu	37	7	44341377	44341377	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44341377delA	uc003tkq.2	-						CAMK2B_uc003tkp.2_Intron|CAMK2B_uc003tkx.2_Intron|CAMK2B_uc010kyd.2_Intron|CAMK2B_uc003tkr.2_Intron|CAMK2B_uc003tks.2_Intron|CAMK2B_uc003tku.2_Intron|CAMK2B_uc003tkv.2_Intron|CAMK2B_uc003tkt.2_Intron|CAMK2B_uc003tkw.2_Intron|CAMK2B_uc010kyc.2_Intron	NM_001220	NP_001211			calcium/calmodulin-dependent protein kinase II						interferon-gamma-mediated signaling pathway|synaptic transmission	cytosol|endocytic vesicle membrane|nucleoplasm|plasma membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			large_intestine(1)|ovary(1)	2																		---	---	---	---
DDX56	54606	broad.mit.edu	37	7	44614349	44614350	+	5'Flank	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44614349_44614350delGT	uc003tlg.2	-						DDX56_uc003tle.2_5'Flank|DDX56_uc003tlf.2_5'Flank|DDX56_uc003tlh.2_5'Flank|DDX56_uc010kyg.2_5'Flank|DDX56_uc010kyh.1_5'Flank	NM_019082	NP_061955			DEAD (Asp-Glu-Ala-Asp) box polypeptide 56						rRNA processing	nucleolus	ATP binding|ATP-dependent RNA helicase activity|identical protein binding|RNA binding			upper_aerodigestive_tract(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	44769352	44769352	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44769352delT								OGDH (20684 upstream) : ZMIZ2 (18828 downstream)																																			---	---	---	---
CCM2	83605	broad.mit.edu	37	7	45068388	45068390	+	Intron	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45068388_45068390delAAA	uc003tmo.2	+						CCM2_uc003tmn.2_Intron|CCM2_uc003tmp.2_Intron|CCM2_uc003tmq.2_Intron|CCM2_uc003tmr.2_Intron|CCM2_uc011kcb.1_Intron|CCM2_uc011kcc.1_Intron|CCM2_uc003tms.2_Intron	NM_031443	NP_113631			cerebral cavernous malformation 2 isoform 2						endothelial tube morphogenesis|integrin-mediated signaling pathway|stress-activated MAPK cascade|vasculogenesis	cytoplasm	protein binding				0														Familial_Cerebral_Cavernous_Angioma				---	---	---	---
ADCY1	107	broad.mit.edu	37	7	45650357	45650359	+	Intron	DEL	GTA	-	-	rs111882564	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45650357_45650359delGTA	uc003tne.3	+						ADCY1_uc003tnd.2_Intron	NM_021116	NP_066939			adenylate cyclase 1						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|calmodulin binding|metal ion binding			ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	6					Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	47634407	47634407	+	IGR	DEL	T	-	-	rs78812322	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47634407delT								TNS3 (12665 upstream) : C7orf65 (60435 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	47643911	47643912	+	IGR	INS	-	A	A	rs113085111		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47643911_47643912insA								TNS3 (22169 upstream) : C7orf65 (50930 downstream)																																			---	---	---	---
PKD1L1	168507	broad.mit.edu	37	7	47855453	47855453	+	Intron	DEL	A	-	-	rs76920480		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47855453delA	uc003tny.1	-						C7orf69_uc003tnz.3_Intron|C7orf69_uc003toa.1_Intron|PKD1L1_uc003tob.2_Intron	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	48773400	48773400	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48773400delT								ABCA13 (86309 upstream) : CDC14C (190757 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	48983213	48983213	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48983213delT								CDC14C (16164 upstream) : VWC2 (830044 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	49310370	49310370	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49310370delT								CDC14C (343321 upstream) : VWC2 (502887 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	49423646	49423647	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49423646_49423647delTG								CDC14C (456597 upstream) : VWC2 (389610 downstream)																																			---	---	---	---
ZPBP	11055	broad.mit.edu	37	7	50079452	50079455	+	Intron	DEL	ACAG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50079452_50079455delACAG	uc003tou.2	-						ZPBP_uc011kci.1_Intron|ZPBP_uc010kyw.2_Intron	NM_007009	NP_008940			zona pellucida binding protein isoform 1						binding of sperm to zona pellucida	extracellular region					0	Glioma(55;0.08)|all_neural(89;0.245)																	---	---	---	---
COBL	23242	broad.mit.edu	37	7	51176929	51176929	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51176929delT	uc003tpr.3	-						COBL_uc003tps.2_Intron|COBL_uc011kcl.1_Intron|COBL_uc010kzc.2_Intron|COBL_uc003tpt.2_Intron|COBL_uc003tpp.3_Intron|COBL_uc003tpq.3_Intron	NM_015198	NP_056013			cordon-bleu homolog											skin(3)|ovary(2)	5	Glioma(55;0.08)																	---	---	---	---
COBL	23242	broad.mit.edu	37	7	51257912	51257912	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51257912delT	uc003tpr.3	-						COBL_uc003tps.2_Intron|COBL_uc011kcl.1_Intron|COBL_uc010kzc.2_Intron|COBL_uc003tpt.2_Intron|COBL_uc003tpp.3_Intron|COBL_uc003tpq.3_Intron	NM_015198	NP_056013			cordon-bleu homolog											skin(3)|ovary(2)	5	Glioma(55;0.08)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	51553667	51553667	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51553667delT								COBL (169152 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	52451529	52451529	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52451529delA								None (None upstream) : POM121L12 (651820 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	52933919	52933919	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52933919delA								None (None upstream) : POM121L12 (169430 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53054311	53054311	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53054311delA								None (None upstream) : POM121L12 (49038 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53226612	53226612	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53226612delT								POM121L12 (121995 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53987539	53987539	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53987539delT								POM121L12 (882922 upstream) : HPVC1 (281378 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	54199046	54199046	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54199046delG								None (None upstream) : HPVC1 (69871 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	54897675	54897675	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54897675delA								SEC61G (70736 upstream) : EGFR (189050 downstream)																																			---	---	---	---
EGFR	1956	broad.mit.edu	37	7	55144105	55144105	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55144105delA	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)			---	---	---	---
EGFR	1956	broad.mit.edu	37	7	55147282	55147285	+	Intron	DEL	TTTG	-	-	rs34784599		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55147282_55147285delTTTG	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)			---	---	---	---
FKBP9L	360132	broad.mit.edu	37	7	55749943	55749943	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55749943delA	uc010kzl.2	-	6					FKBP9L_uc010kzk.2_3'UTR|FKBP9L_uc003tqt.2_3'UTR|FKBP9L_uc011kcs.1_3'UTR	NR_003949				SubName: Full=cDNA, FLJ79189, highly similar to FK506-binding protein 9 (EC 5.2.1.8);												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	55845355	55845355	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55845355delT								FKBP9L (73095 upstream) : SEPT14 (15882 downstream)																																			---	---	---	---
SEPT14	346288	broad.mit.edu	37	7	55872886	55872886	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55872886delA	uc003tqz.2	-							NM_207366	NP_997249			septin 14						cell cycle|cell division	septin complex	GTP binding|protein binding				0	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)															---	---	---	---
SEPT14	346288	broad.mit.edu	37	7	55910601	55910601	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55910601delA	uc003tqz.2	-							NM_207366	NP_997249			septin 14						cell cycle|cell division	septin complex	GTP binding|protein binding				0	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	56431685	56431686	+	IGR	INS	-	AT	AT			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56431685_56431686insAT								PSPH (247595 upstream) : DKFZp434L192 (132230 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	56812543	56812544	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56812543_56812544delTT								DKFZp434L192 (247566 upstream) : ZNF479 (374784 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57126086	57126086	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57126086delA								DKFZp434L192 (561109 upstream) : ZNF479 (61242 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57274993	57274993	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57274993delT								ZNF479 (67422 upstream) : ZNF716 (234890 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57374360	57374360	+	IGR	DEL	A	-	-	rs112092285		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57374360delA								ZNF479 (166789 upstream) : ZNF716 (135523 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57461408	57461408	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57461408delA								ZNF479 (253837 upstream) : ZNF716 (48475 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57548983	57548992	+	IGR	DEL	ATCAAATGGA	-	-	rs112209640		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57548983_57548992delATCAAATGGA								ZNF716 (15718 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57634082	57634083	+	IGR	INS	-	AC	AC	rs138123622	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57634082_57634083insAC								ZNF716 (100817 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61757468	61757469	+	IGR	INS	-	ATG	ATG	rs141732065	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61757468_61757469insATG								None (None upstream) : LOC643955 (994203 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61794281	61794281	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61794281delG								None (None upstream) : LOC643955 (957391 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61794323	61794324	+	IGR	INS	-	AAC	AAC			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61794323_61794324insAAC								None (None upstream) : LOC643955 (957348 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61820176	61820177	+	IGR	INS	-	T	T	rs147475889	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61820176_61820177insT								None (None upstream) : LOC643955 (931495 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61866347	61866347	+	IGR	DEL	T	-	-	rs111371066		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61866347delT								None (None upstream) : LOC643955 (885325 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61893981	61893982	+	IGR	INS	-	A	A	rs138035920	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61893981_61893982insA								None (None upstream) : LOC643955 (857690 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62106521	62106522	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62106521_62106522insT								None (None upstream) : LOC643955 (645150 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62476748	62476749	+	IGR	INS	-	T	T	rs138163797	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62476748_62476749insT								None (None upstream) : LOC643955 (274923 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62730822	62730822	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62730822delA								None (None upstream) : LOC643955 (20850 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62964754	62964755	+	IGR	DEL	TT	-	-	rs75520005		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62964754_62964755delTT								LOC100287704 (152603 upstream) : ZNF727 (541066 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62989363	62989364	+	IGR	INS	-	T	T	rs141102390		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62989363_62989364insT								LOC100287704 (177212 upstream) : ZNF727 (516457 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	63120881	63120881	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63120881delT								LOC100287704 (308730 upstream) : ZNF727 (384940 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	63549842	63549842	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63549842delT								ZNF727 (10917 upstream) : ZNF735 (117739 downstream)																																			---	---	---	---
ZNF138	7697	broad.mit.edu	37	7	64253581	64253582	+	5'Flank	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64253581_64253582insT	uc011kdp.1	+						ZNF138_uc003ttg.2_5'Flank|ZNF138_uc011kdq.1_5'Flank|ZNF138_uc003tth.2_5'Flank|ZNF138_uc010kzs.2_5'Flank	NM_001160183	NP_001153655			zinc finger protein 138 isoform 2						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding				0		Lung NSC(55;0.0795)|all_lung(88;0.18)																---	---	---	---
INTS4L1	285905	broad.mit.edu	37	7	64683071	64683071	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64683071delA	uc003ttw.2	+							NR_027393				Homo sapiens cDNA FLJ25037 fis, clone CBL03066.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	64709270	64709270	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64709270delT								INTS4L1 (14671 upstream) : ZNF92 (129498 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	65133884	65133885	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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	65281408	65281408	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65281408delA								CCT6P1 (52747 upstream) : VKORC1L1 (56849 downstream)																																			---	---	---	---
TPST1	8460	broad.mit.edu	37	7	65732951	65732951	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65732951delT	uc003tuw.2	+						TPST1_uc010kzy.2_Intron|TPST1_uc010kzz.2_Intron|TPST1_uc010laa.2_Intron	NM_003596	NP_003587			tyrosylprotein sulfotransferase 1						inflammatory response|peptidyl-tyrosine sulfation	Golgi membrane|integral to membrane|membrane fraction	protein-tyrosine sulfotransferase activity				0																		---	---	---	---
TPST1	8460	broad.mit.edu	37	7	65751137	65751137	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65751137delT	uc003tuw.2	+						TPST1_uc010kzy.2_Intron|TPST1_uc010kzz.2_Intron|TPST1_uc010laa.2_Intron	NM_003596	NP_003587			tyrosylprotein sulfotransferase 1						inflammatory response|peptidyl-tyrosine sulfation	Golgi membrane|integral to membrane|membrane fraction	protein-tyrosine sulfotransferase activity				0																		---	---	---	---
TPST1	8460	broad.mit.edu	37	7	65805208	65805208	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65805208delA	uc003tuw.2	+						TPST1_uc010kzy.2_Intron|TPST1_uc010kzz.2_Intron|TPST1_uc010laa.2_Intron	NM_003596	NP_003587			tyrosylprotein sulfotransferase 1						inflammatory response|peptidyl-tyrosine sulfation	Golgi membrane|integral to membrane|membrane fraction	protein-tyrosine sulfotransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	66381892	66381892	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66381892delA								LOC729156 (72079 upstream) : C7orf42 (4311 downstream)																																			---	---	---	---
TYW1	55253	broad.mit.edu	37	7	66669492	66669492	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66669492delT	uc003tvn.2	+						TYW1_uc010lai.2_Intron|TYW1_uc011kef.1_Intron|PMS2L4_uc003tvo.2_Intron	NM_018264	NP_060734			radical S-adenosyl methionine and flavodoxin						tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity			skin(1)	1		Lung NSC(55;0.0846)|all_lung(88;0.183)																---	---	---	---
Unknown	0	broad.mit.edu	37	7	67347928	67347928	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67347928delC								STAG3L4 (561416 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67469938	67469938	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67469938delT								STAG3L4 (683426 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67729993	67729993	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67729993delA								STAG3L4 (943481 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67810347	67810347	+	IGR	DEL	C	-	-	rs13226586	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67810347delC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68293418	68293418	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68293418delA								None (None upstream) : AUTS2 (770487 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68302635	68302635	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68302635delG								None (None upstream) : AUTS2 (761270 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68770663	68770664	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68770663_68770664delTC								None (None upstream) : AUTS2 (293241 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68909971	68909973	+	IGR	DEL	TTG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68909971_68909973delTTG								None (None upstream) : AUTS2 (153932 downstream)																																			---	---	---	---
AUTS2	26053	broad.mit.edu	37	7	69480846	69480846	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69480846delT	uc003tvw.3	+						AUTS2_uc003tvv.3_Intron|AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385			autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)														---	---	---	---
AUTS2	26053	broad.mit.edu	37	7	69552550	69552550	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69552550delT	uc003tvw.3	+						AUTS2_uc003tvv.3_Intron|AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385			autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)														---	---	---	---
AUTS2	26053	broad.mit.edu	37	7	69944624	69944624	+	Intron	DEL	A	-	-	rs66623978		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69944624delA	uc003tvw.3	+						AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385			autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)														---	---	---	---
WBSCR17	64409	broad.mit.edu	37	7	70713173	70713174	+	Intron	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70713173_70713174delAG	uc003tvy.2	+							NM_022479	NP_071924			UDP-GalNAc:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)																---	---	---	---
WBSCR17	64409	broad.mit.edu	37	7	71026948	71026949	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71026948_71026949delTT	uc003tvy.2	+						WBSCR17_uc003tvz.2_Intron	NM_022479	NP_071924			UDP-GalNAc:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)																---	---	---	---
WBSCR17	64409	broad.mit.edu	37	7	71053855	71053855	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71053855delA	uc003tvy.2	+						WBSCR17_uc003tvz.2_Intron	NM_022479	NP_071924			UDP-GalNAc:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)																---	---	---	---
WBSCR17	64409	broad.mit.edu	37	7	71141960	71141960	+	Intron	DEL	G	-	-	rs115991236	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71141960delG	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	71178999	71178999	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71178999delA								WBSCR17 (416 upstream) : CALN1 (65478 downstream)																																			---	---	---	---
CALN1	83698	broad.mit.edu	37	7	71312665	71312665	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71312665delA	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	71576451	71576451	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71576451delT	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	71689014	71689014	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71689014delA	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	71803599	71803599	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71803599delT	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)																---	---	---	---
POM121	9883	broad.mit.edu	37	7	72398749	72398750	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72398749_72398750delAA	uc003twk.2	+						POM121_uc003twj.2_Intron|POM121_uc010lam.1_Intron	NM_172020	NP_742017			nuclear pore membrane protein 121						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	endoplasmic reticulum membrane|nuclear membrane|nuclear pore					0		Lung NSC(55;0.163)																---	---	---	---
Unknown	0	broad.mit.edu	37	7	72835068	72835069	+	IGR	DEL	AA	-	-	rs79101532		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72835068_72835069delAA								FKBP6 (62427 upstream) : FZD9 (13040 downstream)																																			---	---	---	---
BAZ1B	9031	broad.mit.edu	37	7	72865483	72865483	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72865483delA	uc003tyc.2	-							NM_032408	NP_115784			bromodomain adjacent to zinc finger domain, 1B						ATP-dependent chromatin remodeling|chromatin-mediated maintenance of transcription|DNA replication-dependent nucleosome disassembly|double-strand break repair|heart morphogenesis|transcription, DNA-dependent	WINAC complex	ATP binding|chromatin binding|histone acetyl-lysine binding|histone kinase activity|non-membrane spanning protein tyrosine kinase activity|protein complex scaffold|vitamin D receptor activator activity|vitamin D receptor binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	7		Lung NSC(55;0.0659)|all_lung(88;0.152)																---	---	---	---
BAZ1B	9031	broad.mit.edu	37	7	72869194	72869194	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72869194delT	uc003tyc.2	-							NM_032408	NP_115784			bromodomain adjacent to zinc finger domain, 1B						ATP-dependent chromatin remodeling|chromatin-mediated maintenance of transcription|DNA replication-dependent nucleosome disassembly|double-strand break repair|heart morphogenesis|transcription, DNA-dependent	WINAC complex	ATP binding|chromatin binding|histone acetyl-lysine binding|histone kinase activity|non-membrane spanning protein tyrosine kinase activity|protein complex scaffold|vitamin D receptor activator activity|vitamin D receptor binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	7		Lung NSC(55;0.0659)|all_lung(88;0.152)																---	---	---	---
Unknown	0	broad.mit.edu	37	7	73051806	73051809	+	IGR	DEL	AAAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73051806_73051809delAAAA								MLXIPL (12936 upstream) : VPS37D (30365 downstream)																																			---	---	---	---
RFC2	5982	broad.mit.edu	37	7	73158228	73158228	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73158228delT	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	73413340	73413340	+	Intron	DEL	A	-	-	rs72466021		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73413340delA	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																		---	---	---	---
EIF4H	7458	broad.mit.edu	37	7	73601779	73601779	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73601779delT	uc003uad.1	+						RFC2_uc011kfa.1_Intron|EIF4H_uc011kfg.1_Intron|EIF4H_uc010lbm.2_Intron|EIF4H_uc003uae.1_Intron|EIF4H_uc003uaf.1_Intron	NM_022170	NP_071496			eukaryotic translation initiation factor 4H						interspecies interaction between organisms|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex|perinuclear region of cytoplasm	nucleotide binding|protein binding|translation initiation factor activity				0																		---	---	---	---
RFC2	5982	broad.mit.edu	37	7	73665125	73665125	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73665125delT	uc003uaj.2	-						RFC2_uc011kfa.1_Intron|RFC2_uc003uak.2_Intron|RFC2_uc010lbp.2_Intron|RFC2_uc003ual.2_Intron	NM_181471	NP_852136			replication factor C 2 isoform 1						cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			liver(1)|central_nervous_system(1)	2																		---	---	---	---
CLIP2	7461	broad.mit.edu	37	7	73732478	73732478	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73732478delA	uc003uam.2	+						CLIP2_uc003uan.2_Intron	NM_003388	NP_003379			CAP-GLY domain containing linker protein 2							microtubule associated complex				skin(3)	3																		---	---	---	---
GTF2IRD1	9569	broad.mit.edu	37	7	74004033	74004035	+	Intron	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74004033_74004035delAAA	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																		---	---	---	---
GTF2I	2969	broad.mit.edu	37	7	74105135	74105135	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74105135delT	uc003uau.2	+						GTF2I_uc003uat.2_Intron|GTF2I_uc003uav.2_Intron|GTF2I_uc003uaw.2_Intron|GTF2I_uc003uay.2_Intron|GTF2I_uc003uax.2_Intron	NM_032999	NP_127492			general transcription factor IIi isoform 1						negative regulation of angiogenesis|signal transduction|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	74286262	74286262	+	IGR	DEL	T	-	-	rs111433198	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74286262delT								GTF2IRD2 (18421 upstream) : STAG3L2 (12584 downstream)																																			---	---	---	---
HIP1	3092	broad.mit.edu	37	7	75185123	75185124	+	Intron	INS	-	A	A	rs146728911	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75185123_75185124insA	uc003uds.1	-						HIP1_uc011kfz.1_Intron	NM_005338	NP_005329			huntingtin interacting protein 1						activation of caspase activity|cell differentiation|clathrin coat assembly|endocytosis|induction of apoptosis|positive regulation of receptor-mediated endocytosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	clathrin coated vesicle membrane|cytoskeleton|Golgi apparatus|membrane fraction|nucleus	actin binding|clathrin binding|phosphatidylinositol binding|structural constituent of cytoskeleton			lung(3)|pancreas(2)|ovary(1)|breast(1)|central_nervous_system(1)	8								T	PDGFRB	CMML								---	---	---	---
HIP1	3092	broad.mit.edu	37	7	75224601	75224602	+	Intron	INS	-	CTTTCTTTCTTTTTCTCT	CTTTCTTTCTTTTTCTCT	rs146767440	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75224601_75224602insCTTTCTTTCTTTTTCTCT	uc003uds.1	-						HIP1_uc011kfz.1_5'Flank	NM_005338	NP_005329			huntingtin interacting protein 1						activation of caspase activity|cell differentiation|clathrin coat assembly|endocytosis|induction of apoptosis|positive regulation of receptor-mediated endocytosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	clathrin coated vesicle membrane|cytoskeleton|Golgi apparatus|membrane fraction|nucleus	actin binding|clathrin binding|phosphatidylinositol binding|structural constituent of cytoskeleton			lung(3)|pancreas(2)|ovary(1)|breast(1)|central_nervous_system(1)	8								T	PDGFRB	CMML								---	---	---	---
HIP1	3092	broad.mit.edu	37	7	75284743	75284743	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75284743delA	uc003uds.1	-							NM_005338	NP_005329			huntingtin interacting protein 1						activation of caspase activity|cell differentiation|clathrin coat assembly|endocytosis|induction of apoptosis|positive regulation of receptor-mediated endocytosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	clathrin coated vesicle membrane|cytoskeleton|Golgi apparatus|membrane fraction|nucleus	actin binding|clathrin binding|phosphatidylinositol binding|structural constituent of cytoskeleton			lung(3)|pancreas(2)|ovary(1)|breast(1)|central_nervous_system(1)	8								T	PDGFRB	CMML								---	---	---	---
HIP1	3092	broad.mit.edu	37	7	75344769	75344770	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75344769_75344770delAC	uc003uds.1	-							NM_005338	NP_005329			huntingtin interacting protein 1						activation of caspase activity|cell differentiation|clathrin coat assembly|endocytosis|induction of apoptosis|positive regulation of receptor-mediated endocytosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	clathrin coated vesicle membrane|cytoskeleton|Golgi apparatus|membrane fraction|nucleus	actin binding|clathrin binding|phosphatidylinositol binding|structural constituent of cytoskeleton			lung(3)|pancreas(2)|ovary(1)|breast(1)|central_nervous_system(1)	8								T	PDGFRB	CMML								---	---	---	---
HIP1	3092	broad.mit.edu	37	7	75358428	75358428	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75358428delA	uc003uds.1	-							NM_005338	NP_005329			huntingtin interacting protein 1						activation of caspase activity|cell differentiation|clathrin coat assembly|endocytosis|induction of apoptosis|positive regulation of receptor-mediated endocytosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	clathrin coated vesicle membrane|cytoskeleton|Golgi apparatus|membrane fraction|nucleus	actin binding|clathrin binding|phosphatidylinositol binding|structural constituent of cytoskeleton			lung(3)|pancreas(2)|ovary(1)|breast(1)|central_nervous_system(1)	8								T	PDGFRB	CMML								---	---	---	---
Unknown	0	broad.mit.edu	37	7	75483568	75483569	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75483568_75483569delAA								CCL24 (40535 upstream) : RHBDD2 (24748 downstream)																																			---	---	---	---
POR	5447	broad.mit.edu	37	7	75591332	75591333	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75591332_75591333delAA	uc003udy.2	+							NM_000941	NP_000932			cytochrome P450 reductase						cellular organofluorine metabolic process|positive regulation of monooxygenase activity	endoplasmic reticulum membrane	iron ion binding|NADPH-hemoprotein reductase activity			central_nervous_system(1)	1					Benzphetamine(DB00865)|Daunorubicin(DB00694)|Lipoic Acid(DB00166)|Menadione(DB00170)|Methoxyflurane(DB01028)|Mitomycin(DB00305)|Nilutamide(DB00665)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	75791193	75791193	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75791193delT								MDH2 (95265 upstream) : SRRM3 (40023 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	76135779	76135779	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76135779delA								DTX2 (468 upstream) : UPK3B (3966 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	76233503	76233503	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76233503delT	uc003ufs.1	+											Homo sapiens hypothetical LOC554248, mRNA (cDNA clone MGC:87732 IMAGE:5768316), complete cds.																														---	---	---	---
PMS2L11	441263	broad.mit.edu	37	7	76626816	76626817	+	Intron	INS	-	GAGGTGT	GAGGTGT			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76626816_76626817insGAGGTGT	uc003ufw.3	+						PMS2L11_uc011kgn.1_Intron	NR_023383				Homo sapiens cDNA FLJ59034 complete cds, moderately similar to Protein deltex-2.												0																		---	---	---	---
PION	54103	broad.mit.edu	37	7	76985105	76985113	+	Intron	DEL	TTTTTTTTT	-	-	rs148300900		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76985105_76985113delTTTTTTTTT	uc003ugf.2	-						PION_uc003ugg.1_Intron	NM_017439	NP_059135			pigeon homolog						beta-amyloid formation|regulation of proteolysis	trans-Golgi network	beta-amyloid binding			central_nervous_system(1)	1																		---	---	---	---
MAGI2	9863	broad.mit.edu	37	7	77674023	77674024	+	Intron	DEL	CA	-	-	rs71085505		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77674023_77674024delCA	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron	NM_012301	NP_036433			membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)																---	---	---	---
MAGI2	9863	broad.mit.edu	37	7	77815110	77815110	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77815110delT	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron|MAGI2_uc010ldx.1_Intron|MAGI2_uc010ldy.1_Intron	NM_012301	NP_036433			membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)																---	---	---	---
MAGI2	9863	broad.mit.edu	37	7	78275054	78275056	+	Intron	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78275054_78275056delTTT	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron|MAGI2_uc011kgr.1_Intron|MAGI2_uc011kgs.1_Intron	NM_012301	NP_036433			membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)																---	---	---	---
MAGI2	9863	broad.mit.edu	37	7	78650082	78650084	+	Intron	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78650082_78650084delAAA	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron	NM_012301	NP_036433			membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)																---	---	---	---
GNAI1	2770	broad.mit.edu	37	7	79785047	79785047	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79785047delA	uc003uhb.1	+						GNAI1_uc011kgt.1_Intron	NM_002069	NP_002060			guanine nucleotide binding protein (G protein),						cell cycle|cell division|inhibition of adenylate cyclase activity by G-protein signaling pathway|platelet activation|synaptic transmission	centrosome|heterotrimeric G-protein complex|midbody|nucleus	G-protein beta/gamma-subunit complex binding|GTP binding|metabotropic serotonin receptor binding|signal transducer activity			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
CD36	948	broad.mit.edu	37	7	80086804	80086804	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:80086804delA	uc003uhc.2	+							NM_001127444	NP_001120916			CD36 antigen						cell adhesion|cGMP-mediated signaling|cholesterol transport|lipid metabolic process|lipid storage|lipoprotein transport|low-density lipoprotein particle clearance|nitric oxide mediated signal transduction|plasma membrane long-chain fatty acid transport|platelet activation|platelet degranulation|positive regulation of cell-matrix adhesion|positive regulation of macrophage derived foam cell differentiation	integral to plasma membrane|membrane fraction|platelet alpha granule membrane	lipid binding|low-density lipoprotein receptor activity|thrombospondin receptor activity|transforming growth factor beta binding			ovary(1)	1																		---	---	---	---
CD36	948	broad.mit.edu	37	7	80117132	80117132	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:80117132delT	uc003uhc.2	+						GNAT3_uc011kgu.1_Intron	NM_001127444	NP_001120916			CD36 antigen						cell adhesion|cGMP-mediated signaling|cholesterol transport|lipid metabolic process|lipid storage|lipoprotein transport|low-density lipoprotein particle clearance|nitric oxide mediated signal transduction|plasma membrane long-chain fatty acid transport|platelet activation|platelet degranulation|positive regulation of cell-matrix adhesion|positive regulation of macrophage derived foam cell differentiation	integral to plasma membrane|membrane fraction|platelet alpha granule membrane	lipid binding|low-density lipoprotein receptor activity|thrombospondin receptor activity|transforming growth factor beta binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	80913487	80913487	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:80913487delT								SEMA3C (361812 upstream) : HGF (417958 downstream)																																			---	---	---	---
HGF	3082	broad.mit.edu	37	7	81350259	81350259	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81350259delA	uc003uhl.2	-						HGF_uc003uhm.2_Intron	NM_000601	NP_000592			hepatocyte growth factor isoform 1						epithelial to mesenchymal transition|mitosis|platelet activation|platelet degranulation|proteolysis|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling	platelet alpha granule lumen	growth factor activity|serine-type endopeptidase activity			ovary(2)|central_nervous_system(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	82130396	82130399	+	IGR	DEL	AAGA	-	-	rs72075802		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82130396_82130399delAAGA								CACNA2D1 (57365 upstream) : PCLO (252922 downstream)																																			---	---	---	---
PCLO	27445	broad.mit.edu	37	7	82764117	82764118	+	Frame_Shift_Ins	INS	-	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82764117_82764118insG	uc003uhx.2	-	3	3037_3038	c.2748_2749insC	c.(2746-2751)CCCAAAfs	p.P916fs	PCLO_uc003uhv.2_Frame_Shift_Ins_p.P916fs	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	862_863	Pro-rich.				cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7																		---	---	---	---
SEMA3E	9723	broad.mit.edu	37	7	83147686	83147687	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83147686_83147687insA	uc003uhy.1	-							NM_012431	NP_036563			semaphorin 3E precursor						axon guidance	extracellular space|membrane	receptor activity			ovary(3)	3		Medulloblastoma(109;0.109)																---	---	---	---
SEMA3E	9723	broad.mit.edu	37	7	83150140	83150140	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83150140delT	uc003uhy.1	-							NM_012431	NP_036563			semaphorin 3E precursor						axon guidance	extracellular space|membrane	receptor activity			ovary(3)	3		Medulloblastoma(109;0.109)																---	---	---	---
SEMA3A	10371	broad.mit.edu	37	7	83805869	83805869	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83805869delA	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	85905159	85905162	+	IGR	DEL	ACTC	-	-	rs146207288		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:85905159_85905162delACTC								None (None upstream) : GRM3 (368068 downstream)																																			---	---	---	---
ZNF804B	219578	broad.mit.edu	37	7	88578632	88578634	+	Intron	DEL	CTA	-	-	rs71692942		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88578632_88578634delCTA	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	89474491	89474491	+	IGR	DEL	C	-	-	rs34697890		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89474491delC								ZNF804B (508147 upstream) : DPY19L2P4 (274223 downstream)																																			---	---	---	---
GTPBP10	85865	broad.mit.edu	37	7	90004512	90004512	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90004512delA	uc003ukm.1	+						GTPBP10_uc003uki.1_Intron|GTPBP10_uc003ukj.1_Intron|GTPBP10_uc003ukk.1_Intron|GTPBP10_uc003ukl.1_Intron|GTPBP10_uc003ukn.1_Intron|GTPBP10_uc003uko.1_Intron	NM_033107	NP_149098			GTP-binding protein 10 isoform 2						ribosome biogenesis	chromosome|nucleolus	GTP binding|GTPase activity|magnesium ion binding				0																		---	---	---	---
CDK14	5218	broad.mit.edu	37	7	90319301	90319302	+	Intron	INS	-	A	A	rs138868116	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90319301_90319302insA	uc003uky.2	+						CDK14_uc003ukt.1_Intron|CDK14_uc003ukv.1_Intron|CDK14_uc003uku.1_Intron|CDK14_uc003ukx.1_Intron	NM_012395	NP_036527			PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4																		---	---	---	---
CDK14	5218	broad.mit.edu	37	7	90778599	90778602	+	Intron	DEL	AAAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90778599_90778602delAAAA	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	90870782	90870783	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90870782_90870783delTT								CDK14 (30878 upstream) : FZD1 (23000 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	90906460	90906460	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90906460delA								FZD1 (8329 upstream) : MTERF (525000 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	90993777	90993778	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90993777_90993778insA								FZD1 (95646 upstream) : MTERF (437682 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	91542387	91542387	+	IGR	DEL	T	-	-	rs141202019		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91542387delT								MTERF (32371 upstream) : AKAP9 (27802 downstream)																																			---	---	---	---
AKAP9	10142	broad.mit.edu	37	7	91641672	91641672	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91641672delA	uc003ulg.2	+						AKAP9_uc003ule.2_Intron|AKAP9_uc003ulf.2_Intron|AKAP9_uc003uli.2_Intron	NM_005751	NP_005742			A-kinase anchor protein 9 isoform 2						G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)					T	BRAF	papillary thyroid								---	---	---	---
CYP51A1	1595	broad.mit.edu	37	7	91799384	91799384	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91799384delA	uc003uln.3	-						uc003ulo.1_Intron|LOC401387_uc011kho.1_Intron	NM_001146152	NP_001139624			cytochrome P450, family 51, subfamily A,						cholesterol biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	electron carrier activity|heme binding|sterol 14-demethylase activity				0	all_cancers(62;2.16e-09)|all_epithelial(64;3.86e-08)|Breast(17;0.00206)|all_lung(186;0.169)|all_hematologic(106;0.215)|Lung NSC(181;0.227)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)		Fluconazole(DB00196)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Miconazole(DB01110)|Terconazole(DB00251)													---	---	---	---
ANKIB1	54467	broad.mit.edu	37	7	91937039	91937039	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91937039delT	uc003ulw.2	+							NM_019004	NP_061877			ankyrin repeat and IBR domain containing 1								protein binding|zinc ion binding			lung(1)	1	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)															---	---	---	---
PEX1	5189	broad.mit.edu	37	7	92136560	92136560	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92136560delT	uc003uly.2	-						PEX1_uc011khr.1_Intron|PEX1_uc010ley.2_Intron|PEX1_uc011khs.1_Intron|PEX1_uc011kht.1_Intron	NM_000466	NP_000457			peroxin1						microtubule-based peroxisome localization|protein import into peroxisome matrix	cytosol|nucleus|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding			ovary(1)|central_nervous_system(1)	2	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)															---	---	---	---
FAM133B	257415	broad.mit.edu	37	7	92207638	92207638	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92207638delT	uc003umc.2	-	4	372	c.271delA	c.(271-273)AGAfs	p.R91fs	FAM133B_uc003umb.2_Frame_Shift_Del_p.R81fs|FAM133B_uc003umd.2_RNA	NM_152789	NP_690002	Q5BKY9	F133B_HUMAN	hypothetical protein LOC257415 isoform 1	91	Lys-rich.|Ser-rich.									ovary(1)	1	all_cancers(62;7.39e-11)|all_epithelial(64;7.03e-10)|Breast(17;0.00201)|all_lung(186;0.0384)|Lung NSC(181;0.053)|all_hematologic(106;0.237)		STAD - Stomach adenocarcinoma(4;6.16e-07)|GBM - Glioblastoma multiforme(5;9.78e-06)|all cancers(6;1.67e-05)|Epithelial(20;0.113)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)															---	---	---	---
CCDC132	55610	broad.mit.edu	37	7	92930610	92930611	+	Intron	DEL	AA	-	-	rs75948999		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92930610_92930611delAA	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)															---	---	---	---
BET1	10282	broad.mit.edu	37	7	93613076	93613076	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93613076delA	uc003une.3	-											Homo sapiens Bet1p homolog (hbet1) mRNA, complete cds.						ER to Golgi vesicle-mediated transport|protein transport	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	protein binding				0	all_cancers(62;2.22e-10)|all_epithelial(64;1.38e-09)|Lung NSC(181;0.218)	Breast(660;0.000162)|Ovarian(593;0.000626)	STAD - Stomach adenocarcinoma(171;0.000967)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	93879828	93879828	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93879828delG								BET1 (246138 upstream) : COL1A2 (144045 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	94001893	94001893	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94001893delT								BET1 (368203 upstream) : COL1A2 (21980 downstream)																																			---	---	---	---
SGCE	8910	broad.mit.edu	37	7	94220934	94220935	+	Intron	INS	-	C	C	rs138844109	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94220934_94220935insC	uc003unl.2	-						SGCE_uc003unk.2_Intron|SGCE_uc003unm.2_Intron|SGCE_uc003unn.2_Intron|SGCE_uc011kic.1_Intron|SGCE_uc011kid.1_Intron	NM_003919	NP_003910			sarcoglycan, epsilon isoform 2						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	94336770	94336771	+	IGR	INS	-	A	A	rs145358998	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94336770_94336771insA								PEG10 (37766 upstream) : PPP1R9A (200178 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	95348429	95348429	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95348429delT								PDK4 (122504 upstream) : DYNC1I1 (53389 downstream)																																			---	---	---	---
DYNC1I1	1780	broad.mit.edu	37	7	95687332	95687333	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95687332_95687333insT	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	95872284	95872285	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95872284_95872285delTT	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)													---	---	---	---
SLC25A13	10165	broad.mit.edu	37	7	95928588	95928588	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95928588delA	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	96485290	96485290	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96485290delT								SHFM1 (146087 upstream) : DLX6AS (112538 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	96722747	96722747	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96722747delT								DLX5 (68604 upstream) : ACN9 (23158 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	96852327	96852327	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96852327delT								ACN9 (41254 upstream) : TAC1 (508944 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	96977564	96977564	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96977564delT								ACN9 (166491 upstream) : TAC1 (383707 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	97085400	97085400	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97085400delA								ACN9 (274327 upstream) : TAC1 (275871 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	98036178	98036179	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98036178_98036179delTT								BAIAP2L1 (5751 upstream) : NPTX2 (210418 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	98141326	98141327	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98141326_98141327delTG								BAIAP2L1 (110899 upstream) : NPTX2 (105270 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	98408891	98408893	+	IGR	DEL	TAG	-	-	rs140739561	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98408891_98408893delTAG								NPTX2 (149710 upstream) : TMEM130 (35219 downstream)																																			---	---	---	---
SMURF1	57154	broad.mit.edu	37	7	98660116	98660116	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98660116delA	uc003upu.1	-						SMURF1_uc003upv.1_Intron|SMURF1_uc003upt.2_Intron	NM_020429	NP_065162			Smad ubiquitination regulatory factor 1 isoform						BMP signaling pathway|cell differentiation|ectoderm development|negative regulation of BMP signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of protein ubiquitination|proteasomal ubiquitin-dependent protein catabolic process|protein export from nucleus|protein localization at cell surface|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|plasma membrane	activin binding|I-SMAD binding|R-SMAD binding|ubiquitin-protein ligase activity			skin(2)|ovary(1)|lung(1)	4	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	98835724	98835724	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98835724delT								KPNA7 (30635 upstream) : MYH16 (35200 downstream)																																			---	---	---	---
ARPC1A	10552	broad.mit.edu	37	7	98936725	98936725	+	Intron	DEL	A	-	-	rs35100977		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98936725delA	uc003upx.1	+						ARPC1A_uc010lfu.1_Intron|ARPC1A_uc003upy.1_Intron|ARPC1A_uc011kit.1_Intron	NM_006409	NP_006400			actin related protein 2/3 complex subunit 1A						actin cytoskeleton organization|regulation of actin filament polymerization	actin cytoskeleton|cytoplasm	actin binding			ovary(1)	1	all_cancers(62;4.46e-09)|all_epithelial(64;3.44e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0258)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
ZKSCAN1	7586	broad.mit.edu	37	7	99612377	99612377	+	5'Flank	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99612377delA	uc003usk.1	+						ZKSCAN1_uc003usj.2_5'Flank|ZKSCAN1_uc003usl.1_5'Flank|ZKSCAN1_uc003usm.1_5'Flank	NM_003439	NP_003430			zinc finger protein 36						viral reproduction	mitochondrion|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)															---	---	---	---
TAF6	6878	broad.mit.edu	37	7	99710344	99710344	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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)																	---	---	---	---
PILRA	29992	broad.mit.edu	37	7	99984125	99984125	+	Intron	DEL	A	-	-	rs77793522		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99984125delA	uc003uuo.1	+						PILRA_uc011kjo.1_Intron|PILRA_uc003uup.1_Intron|PILRA_uc003uuq.1_Intron	NM_013439	NP_038467			paired immunoglobulin-like type 2 receptor alpha						interspecies interaction between organisms	extracellular region|integral to membrane|plasma membrane	protein binding|receptor activity			skin(1)	1	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
EMID2	136227	broad.mit.edu	37	7	101040670	101040670	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101040670delT	uc010lhy.1	+						EMID2_uc003uyo.1_Intron	NM_133457	NP_597714			EMI domain containing 2							collagen				ovary(1)	1	Lung NSC(181;0.215)																	---	---	---	---
EMID2	136227	broad.mit.edu	37	7	101066563	101066563	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101066563delA	uc010lhy.1	+						EMID2_uc003uyo.1_Intron	NM_133457	NP_597714			EMI domain containing 2							collagen				ovary(1)	1	Lung NSC(181;0.215)																	---	---	---	---
CUX1	1523	broad.mit.edu	37	7	101837332	101837333	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101837332_101837333delTT	uc003uyx.3	+						CUX1_uc003uys.3_Intron|CUX1_uc003uyt.2_Intron|CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron	NM_181552	NP_853530			cut-like homeobox 1 isoform a						negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	102021199	102021199	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102021199delA	uc003uzd.1	+						uc003uze.1_Intron|PRKRIP1_uc003uzf.2_Intron|PRKRIP1_uc003uzg.2_Intron|PRKRIP1_uc011kkq.1_Intron	NM_001003686	NP_001003686			SubName: Full=Putative uncharacterized protein PMS2L3;																														---	---	---	---
NAPEPLD	222236	broad.mit.edu	37	7	102789073	102789074	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102789073_102789074delTT	uc003vbc.2	-						NAPEPLD_uc003vbd.2_Intron|NAPEPLD_uc011klj.1_Intron|NAPEPLD_uc003vbe.2_Intron|NAPEPLD_uc003vbf.2_Intron	NM_198990	NP_945341			N-acyl phosphatidylethanolamine phospholipase D						phospholipid catabolic process	membrane	metal ion binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	102933195	102933195	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102933195delT								DPY19L2P2 (12282 upstream) : PMPCB (4678 downstream)																																			---	---	---	---
SLC26A5	375611	broad.mit.edu	37	7	103014757	103014757	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103014757delA	uc003vbz.2	-	20					SLC26A5_uc003vbt.1_Intron|SLC26A5_uc003vbu.1_Intron|SLC26A5_uc003vbv.1_Intron|SLC26A5_uc003vbw.2_RNA|SLC26A5_uc003vbx.2_3'UTR|SLC26A5_uc003vby.2_RNA|SLC26A5_uc010liy.2_RNA	NM_198999	NP_945350			prestin isoform a						regulation of cell shape|sensory perception of sound	integral to membrane	secondary active sulfate transmembrane transporter activity			ovary(1)	1																		---	---	---	---
RELN	5649	broad.mit.edu	37	7	103449846	103449847	+	Intron	DEL	GA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103449846_103449847delGA	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)														---	---	---	---
LHFPL3	375612	broad.mit.edu	37	7	104418201	104418201	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104418201delT	uc003vce.2	+						LHFPL3_uc003vcf.2_Intron	NM_199000	NP_945351			lipoma HMGIC fusion partner-like 3							integral to membrane					0																		---	---	---	---
MLL5	55904	broad.mit.edu	37	7	104719584	104719584	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104719584delT	uc003vcm.2	+						MLL5_uc010lja.1_Intron|MLL5_uc010ljb.1_Intron|MLL5_uc003vcl.2_Intron|MLL5_uc010ljc.2_Intron|MLL5_uc003vco.1_Intron|MLL5_uc010ljd.1_Intron	NM_182931	NP_891847			myeloid/lymphoid or mixed-lineage leukemia 5						cell cycle arrest|cellular response to retinoic acid|DNA methylation|erythrocyte differentiation|neutrophil activation|neutrophil mediated immunity|positive regulation of granulocyte differentiation|positive regulation of transcription, DNA-dependent|retinoic acid receptor signaling pathway|transcription, DNA-dependent	MLL5-L complex|nuclear speck	enzyme binding|histone methyltransferase activity (H3-K4 specific)|transcription coactivator activity|zinc ion binding			ovary(2)|pancreas(1)	3																		---	---	---	---
SRPK2	6733	broad.mit.edu	37	7	105018639	105018639	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105018639delC	uc003vcv.2	-						SRPK2_uc003vcw.1_Intron	NM_182692	NP_872634			serine/arginine-rich protein-specific kinase 2						angiogenesis|cell differentiation|intracellular protein kinase cascade|negative regulation of viral genome replication|nuclear speck organization|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of gene expression|positive regulation of neuron apoptosis|positive regulation of viral genome replication|spliceosome assembly	cytoplasm|nucleolus	14-3-3 protein binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity			central_nervous_system(3)|ovary(2)|upper_aerodigestive_tract(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	105064934	105064934	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105064934delT								SRPK2 (25136 upstream) : PUS7 (32028 downstream)																																			---	---	---	---
ATXN7L1	222255	broad.mit.edu	37	7	105459804	105459804	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105459804delA	uc003vde.2	-						ATXN7L1_uc003vdi.2_Intron	NM_020725	NP_065776			ataxin 7-like 1 isoform 1												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	106015158	106015158	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106015158delA								NAMPT (89520 upstream) : FLJ36031 (283992 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	106367789	106367789	+	Intron	DEL	T	-	-	rs34210749		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106367789delT	uc003vds.2	-											Homo sapiens full length insert cDNA clone ZC44D09.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	106448451	106448451	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106448451delT								FLJ36031 (146860 upstream) : PIK3CG (57272 downstream)																																			---	---	---	---
COG5	10466	broad.mit.edu	37	7	107158147	107158148	+	Intron	DEL	TT	-	-	rs78435328		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107158147_107158148delTT	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																		---	---	---	---
SLC26A3	1811	broad.mit.edu	37	7	107406419	107406419	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107406419delT	uc003ver.2	-						SLC26A3_uc003ves.2_Intron	NM_000111	NP_000102			solute carrier family 26, member 3						excretion	integral to membrane|membrane fraction	inorganic anion exchanger activity|secondary active sulfate transmembrane transporter activity|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			ovary(3)|skin(1)	4																		---	---	---	---
SLC26A3	1811	broad.mit.edu	37	7	107418553	107418553	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107418553delT	uc003ver.2	-						SLC26A3_uc003ves.2_Intron	NM_000111	NP_000102			solute carrier family 26, member 3						excretion	integral to membrane|membrane fraction	inorganic anion exchanger activity|secondary active sulfate transmembrane transporter activity|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			ovary(3)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	107469812	107469812	+	IGR	DEL	T	-	-	rs113951604		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107469812delT								SLC26A3 (26134 upstream) : DLD (61774 downstream)																																			---	---	---	---
LAMB1	3912	broad.mit.edu	37	7	107574049	107574049	+	Intron	DEL	A	-	-	rs74783801		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107574049delA	uc003vew.2	-						LAMB1_uc003vev.2_Intron	NM_002291	NP_002282			laminin, beta 1 precursor						axon guidance|odontogenesis|positive regulation of cell migration|positive regulation of epithelial cell proliferation|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-2 complex|laminin-8 complex|perinuclear region of cytoplasm	extracellular matrix structural constituent			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	8					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
NRCAM	4897	broad.mit.edu	37	7	107965882	107965883	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107965882_107965883delTT	uc003vfb.2	-						NRCAM_uc003vfc.2_Intron|NRCAM_uc011kmk.1_Intron|NRCAM_uc003vfd.2_Intron|NRCAM_uc003vfe.2_Intron	NM_001037132	NP_001032209			neuronal cell adhesion molecule isoform A						angiogenesis|axon guidance|axonal fasciculation|cell-cell adhesion|central nervous system development|clustering of voltage-gated sodium channels|neuron migration|positive regulation of neuron differentiation|regulation of axon extension|synapse assembly	external side of plasma membrane|integral to plasma membrane	ankyrin binding			ovary(3)|breast(2)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	108192708	108192708	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108192708delT								PNPLA8 (24103 upstream) : THAP5 (9965 downstream)																																			---	---	---	---
THAP5	168451	broad.mit.edu	37	7	108205526	108205526	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108205526delT	uc003vfm.2	-	3	451	c.297delA	c.(295-297)AAAfs	p.K99fs	THAP5_uc003vfl.2_Frame_Shift_Del_p.K57fs	NM_001130475	NP_001123947	Q7Z6K1	THAP5_HUMAN	THAP domain containing 5 isoform 1	99					cell cycle|negative regulation of cell cycle	nucleus	DNA binding|metal ion binding|protease binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	108288022	108288022	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108288022delA								DNAJB9 (72730 upstream) : C7orf66 (236018 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	108630004	108630005	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108630004_108630005delAC								C7orf66 (105367 upstream) : EIF3IP1 (969279 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	108948372	108948372	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108948372delA								C7orf66 (423735 upstream) : EIF3IP1 (650912 downstream)																																			---	---	---	---
IMMP2L	83943	broad.mit.edu	37	7	110415863	110415863	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110415863delA	uc003vfq.1	-						IMMP2L_uc010ljr.1_Intron	NM_032549	NP_115938			IMP2 inner mitochondrial membrane protease-like						protein processing involved in protein targeting to mitochondrion|proteolysis	integral to membrane|mitochondrial inner membrane peptidase complex|nucleus	serine-type peptidase activity				0				UCEC - Uterine corpus endometrioid carcinoma (4;0.053)|Epithelial(3;2.27e-07)|all cancers(3;1.36e-05)|STAD - Stomach adenocarcinoma(3;0.00148)|KIRC - Kidney renal clear cell carcinoma(11;0.0339)|Lung(3;0.0375)|Kidney(11;0.0415)|LUSC - Lung squamous cell carcinoma(290;0.173)														---	---	---	---
IMMP2L	83943	broad.mit.edu	37	7	111117547	111117547	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111117547delT	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	111575538	111575538	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111575538delA	uc003vfx.2	-						DOCK4_uc003vfy.2_Intron|DOCK4_uc003vga.1_Intron|DOCK4_uc010ljt.1_Frame_Shift_Del_p.C375fs	NM_014705	NP_055520			dedicator of cytokinesis 4						cell chemotaxis	cytosol|endomembrane system|membrane|stereocilium	GTP binding|guanyl-nucleotide exchange factor activity|PDZ domain binding|Rac GTPase activator activity|Rac GTPase binding|receptor tyrosine kinase binding|SH3 domain binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)	4		Acute lymphoblastic leukemia(1;0.0441)																---	---	---	---
DOCK4	9732	broad.mit.edu	37	7	111675668	111675669	+	Intron	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111675668_111675669delAG	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	7	112227590	112227591	+	IGR	DEL	GA	-	-	rs141202410		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112227590_112227591delGA								C7orf53 (96655 upstream) : TMEM168 (178198 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	112361866	112361867	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112361866_112361867delAC								C7orf53 (230931 upstream) : TMEM168 (43922 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	113014710	113014710	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:113014710delA								LOC401397 (256073 upstream) : PPP1R3A (502172 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	114694618	114694619	+	IGR	INS	-	TT	TT	rs147212842	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114694618_114694619insTT								MDFIC (35355 upstream) : TFEC (880583 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	115449468	115449469	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115449468_115449469delAC								MDFIC (790205 upstream) : TFEC (125733 downstream)																																			---	---	---	---
CAV1	857	broad.mit.edu	37	7	116102792	116102793	+	Intron	INS	-	CACA	CACA	rs138864637	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116102792_116102793insCACA	uc010lkd.1	+						CAV2_uc003vhv.2_Intron|CAV2_uc003vhw.2_Intron|CAV2_uc003vhx.2_Intron|CAV2_uc010lkb.1_Intron|CAV2_uc010lkc.2_Intron|CAV2_uc003vib.2_Intron|CAV2_uc003vhz.2_Intron|CAV2_uc003via.2_Intron|CAV1_uc010lke.1_Intron	NM_001753	NP_001744			caveolin 1						blood coagulation|calcium ion transport|caveola assembly|cellular response to starvation|cholesterol homeostasis|cytosolic calcium ion homeostasis|inactivation of MAPK activity|interspecies interaction between organisms|leukocyte migration|lipid storage|maintenance of protein location in cell|mammary gland involution|membrane depolarization|negative regulation of BMP signaling pathway|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of endothelial cell proliferation|negative regulation of epithelial cell differentiation|negative regulation of nitric oxide biosynthetic process|negative regulation of peptidyl-serine phosphorylation|negative regulation of protein binding|negative regulation of transcription from RNA polymerase II promoter|nitric oxide homeostasis|nitric oxide metabolic process|positive regulation of calcium ion transport into cytosol|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of metalloenzyme activity|positive regulation of peptidyl-serine phosphorylation|positive regulation of vasoconstriction|protein homooligomerization|receptor internalization|regulation of blood coagulation|regulation of fatty acid metabolic process|regulation of nitric-oxide synthase activity|regulation of smooth muscle contraction|response to calcium ion|response to estrogen stimulus|response to hypoxia|response to progesterone stimulus|skeletal muscle tissue development|T cell costimulation|triglyceride metabolic process|vasculogenesis|vesicle organization	apical plasma membrane|basolateral plasma membrane|caveola|caveola|cytosol|endoplasmic reticulum|endosome|Golgi membrane|lipid particle|perinuclear region of cytoplasm	cholesterol binding|nitric-oxide synthase binding|peptidase activator activity|protein binding|protein complex scaffold|receptor binding				0	all_epithelial(6;1.42e-06)|Lung NSC(10;0.0056)|all_lung(10;0.00609)		STAD - Stomach adenocarcinoma(10;0.00878)															---	---	---	---
CAPZA2	830	broad.mit.edu	37	7	116490463	116490465	+	Intron	DEL	AAC	-	-	rs142027310	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116490463_116490465delAAC	uc003vik.1	+											Homo sapiens mRNA for capping protein (actin filament) muscle Z-line, alpha 2 variant, clone: HSI05568.						actin cytoskeleton organization|actin filament capping|blood coagulation|cellular component movement|innate immune response|protein complex assembly	cytosol|extracellular region|F-actin capping protein complex	actin binding				0	all_cancers(3;8.53e-08)|all_epithelial(6;7.79e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)		GBM - Glioblastoma multiforme(2;5.01e-06)|STAD - Stomach adenocarcinoma(10;0.000512)|all cancers(2;0.00326)															---	---	---	---
WNT2	7472	broad.mit.edu	37	7	116926180	116926180	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116926180delA	uc003viz.2	-						WNT2_uc003vja.2_Intron	NM_003391	NP_003382			wingless-type MMTV integration site family						atrial cardiac muscle tissue morphogenesis|canonical Wnt receptor signaling pathway|cardiac epithelial to mesenchymal transition|cellular response to retinoic acid|cellular response to transforming growth factor beta stimulus|dorsal/ventral axis specification|iris morphogenesis|labyrinthine layer blood vessel development|lens development in camera-type eye|lung induction|mammary gland epithelium development|neuron differentiation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of fibroblast proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|Wnt receptor signaling pathway, calcium modulating pathway	cytoplasm|extracellular space|proteinaceous extracellular matrix	cytokine activity|frizzled binding|frizzled-2 binding|signal transducer activity			breast(2)|central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	7	all_epithelial(6;2.24e-06)|Lung NSC(10;0.000936)|all_lung(10;0.00109)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)														---	---	---	---
CFTR	1080	broad.mit.edu	37	7	117276873	117276874	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117276873_117276874delTT	uc003vjd.2	+						CFTR_uc011knq.1_Intron	NM_000492	NP_000483			cystic fibrosis transmembrane conductance						respiratory gaseous exchange	apical plasma membrane|basolateral plasma membrane|chloride channel complex|early endosome membrane	ATP binding|ATP-binding and phosphorylation-dependent chloride channel activity|channel-conductance-controlling ATPase activity|chloride channel regulator activity|enzyme binding|PDZ domain binding			central_nervous_system(2)|skin(2)|ovary(1)	5	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Glibenclamide(DB01016)									Cystic_Fibrosis				---	---	---	---
Unknown	0	broad.mit.edu	37	7	117703410	117703410	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117703410delT								CTTNBP2 (189849 upstream) : NAA38 (120676 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	118018813	118018814	+	IGR	DEL	TG	-	-	rs10247788	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:118018813_118018814delTG								ANKRD7 (136031 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	119763169	119763170	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:119763169_119763170delTT								None (None upstream) : KCND2 (150552 downstream)																																			---	---	---	---
IQUB	154865	broad.mit.edu	37	7	123101773	123101773	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123101773delA	uc003vkn.2	-						IQUB_uc011kny.1_5'Flank|IQUB_uc003vko.2_Intron|IQUB_uc010lkt.2_Intron	NM_178827	NP_849149			IQ motif and ubiquitin domain containing											ovary(3)|large_intestine(1)	4																		---	---	---	---
IQUB	154865	broad.mit.edu	37	7	123142787	123142787	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123142787delT	uc003vkn.2	-	6	1464	c.887delA	c.(886-888)AATfs	p.N296fs	IQUB_uc003vko.2_Frame_Shift_Del_p.N296fs|IQUB_uc010lkt.2_RNA|IQUB_uc003vkp.1_Frame_Shift_Del_p.N296fs|IQUB_uc003vkq.2_3'UTR	NM_178827	NP_849149	Q8NA54	IQUB_HUMAN	IQ motif and ubiquitin domain containing	296										ovary(3)|large_intestine(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	123209457	123209457	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123209457delA								NDUFA5 (11499 upstream) : ASB15 (32464 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	123419987	123419987	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123419987delA								WASL (30871 upstream) : HYALP1 (34206 downstream)																																			---	---	---	---
HYAL4	23553	broad.mit.edu	37	7	123496363	123496363	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123496363delT	uc003vlc.2	+						HYAL4_uc011knz.1_Intron	NM_012269	NP_036401			hyaluronoglucosaminidase 4						fusion of sperm to egg plasma membrane|glycosaminoglycan catabolic process	integral to membrane	hyalurononglucosaminidase activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	124148453	124148453	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124148453delA								TMEM229A (474930 upstream) : GPR37 (237663 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	124149811	124149811	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124149811delT								TMEM229A (476288 upstream) : GPR37 (236305 downstream)																																			---	---	---	---
POT1	25913	broad.mit.edu	37	7	124474968	124474968	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124474968delA	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	124718338	124718339	+	Intron	INS	-	AG	AG	rs146489771	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124718338_124718339insAG	uc010lkx.1	+						uc003vlp.2_Intron|uc003vlq.1_Intron					Homo sapiens cDNA FLJ33356 fis, clone BRACE2005160.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	125230702	125230703	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:125230702_125230703delTT								POT1 (660665 upstream) : GRM8 (847949 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	125400839	125400839	+	IGR	DEL	A	-	-	rs71658307		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:125400839delA								POT1 (830802 upstream) : GRM8 (677813 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	125634230	125634231	+	IGR	INS	-	TCCTTCCTTCCTCCCTCCC	TCCTTCCTTCCTCCCTCCC	rs142205556	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:125634230_125634231insTCCTTCCTTCCTCCCTCCC								None (None upstream) : GRM8 (444421 downstream)																																			---	---	---	---
GRM8	2918	broad.mit.edu	37	7	126519253	126519254	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126519253_126519254delAA	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)			---	---	---	---
FSCN3	29999	broad.mit.edu	37	7	127236658	127236658	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127236658delA	uc003vmd.1	+						FSCN3_uc011koh.1_Intron|FSCN3_uc010llc.1_Intron	NM_020369	NP_065102			fascin 3							actin cytoskeleton|cytoplasm	actin filament binding|protein binding, bridging			ovary(1)	1																		---	---	---	---
SND1	27044	broad.mit.edu	37	7	127534437	127534438	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127534437_127534438delAA	uc003vmi.2	+						SND1_uc010lle.2_Intron	NM_014390	NP_055205			staphylococcal nuclease domain containing 1						gene silencing by RNA|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	melanosome|nucleus|RNA-induced silencing complex	nuclease activity|nucleic acid binding|protein binding|transcription cofactor activity			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
SND1	27044	broad.mit.edu	37	7	127691334	127691334	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127691334delT	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	127740881	127740882	+	IGR	INS	-	TG	TG	rs142452422		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127740881_127740882insTG								SND1 (8223 upstream) : MIR129-1 (107043 downstream)																																			---	---	---	---
LEP	3952	broad.mit.edu	37	7	127885094	127885095	+	Intron	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127885094_127885095delTG	uc003vml.2	+							NM_000230	NP_000221			leptin precursor						adult feeding behavior|energy reserve metabolic process|negative regulation of appetite|placenta development|positive regulation of developmental growth	extracellular space					0																		---	---	---	---
NRF1	4899	broad.mit.edu	37	7	129395139	129395139	+	3'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129395139delT	uc003voz.2	+	11					NRF1_uc003vpa.2_3'UTR|NRF1_uc011kpa.1_3'UTR|NRF1_uc003vpb.2_3'UTR	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																		---	---	---	---
UBE2H	7328	broad.mit.edu	37	7	129583020	129583020	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129583020delT	uc003vpf.1	-						UBE2H_uc003vpg.1_Intron	NM_003344	NP_003335			ubiquitin-conjugating enzyme E2H isoform 1						protein K11-linked ubiquitination|protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process		ATP binding|ubiquitin-protein ligase activity			skin(1)	1	Melanoma(18;0.0435)																	---	---	---	---
ZC3HC1	51530	broad.mit.edu	37	7	129663647	129663648	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129663647_129663648delTT	uc003vpi.2	-						ZC3HC1_uc003vph.2_Intron|ZC3HC1_uc010lma.2_Intron	NM_016478	NP_057562			zinc finger, C3HC type 1						cell division|mitosis	nucleus	protein kinase binding|zinc ion binding				0	Melanoma(18;0.0435)																	---	---	---	---
C7orf45	136263	broad.mit.edu	37	7	129856477	129856477	+	3'UTR	DEL	A	-	-	rs72394033		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129856477delA	uc003vpp.2	+	3						NM_145268	NP_660311			hypothetical protein LOC136263							integral to membrane					0	Melanoma(18;0.0435)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	129891324	129891324	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129891324delT								C7orf45 (34641 upstream) : CPA2 (15379 downstream)																																			---	---	---	---
CPA5	93979	broad.mit.edu	37	7	129983094	129983094	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129983094delT	uc010lmd.1	+						CPA5_uc003vps.2_5'Flank|CPA5_uc003vpt.2_5'Flank|CPA5_uc010lme.1_5'Flank|CPA5_uc003vpu.1_5'Flank	NM_001127441	NP_001120913			carboxypeptidase A5 isoform 1						proteolysis	extracellular region	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2	Melanoma(18;0.0435)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	130109769	130109769	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130109769delT								TSGA14 (28915 upstream) : MEST (16277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	130566196	130566196	+	Intron	DEL	A	-	-	rs142423875		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130566196delA	uc003vql.1	+						uc003vqn.3_RNA					full-length cDNA clone CS0DI009YJ20 of Placenta Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
FLJ43663	378805	broad.mit.edu	37	7	130713056	130713056	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130713056delA	uc011kpk.1	-						FLJ43663_uc003vqo.1_Intron|FLJ43663_uc003vqp.2_Intron|FLJ43663_uc003vqq.2_Intron	NR_024153				Homo sapiens cDNA FLJ43663 fis, clone SYNOV4005989.												0																		---	---	---	---
MKLN1	4289	broad.mit.edu	37	7	131086620	131086620	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131086620delA	uc011kpm.1	+						MKLN1_uc011kpl.1_Intron|MKLN1_uc010lmh.2_Intron|MKLN1_uc003vqs.2_Intron	NM_013255	NP_037387			muskelin 1, intracellular mediator containing						signal transduction	cytoplasm	protein binding			breast(1)	1	Melanoma(18;0.162)																	---	---	---	---
MKLN1	4289	broad.mit.edu	37	7	131134410	131134410	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131134410delT	uc011kpm.1	+						MKLN1_uc011kpl.1_Intron|MKLN1_uc010lmh.2_Intron|MKLN1_uc003vqs.2_Intron	NM_013255	NP_037387			muskelin 1, intracellular mediator containing						signal transduction	cytoplasm	protein binding			breast(1)	1	Melanoma(18;0.162)																	---	---	---	---
PLXNA4	91584	broad.mit.edu	37	7	131946126	131946126	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131946126delT	uc003vra.3	-							NM_020911	NP_065962			plexin A4 isoform 1							integral to membrane|intracellular|plasma membrane				ovary(1)	1																		---	---	---	---
PLXNA4	91584	broad.mit.edu	37	7	132038937	132038938	+	Intron	INS	-	GT	GT	rs138307873	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132038937_132038938insGT	uc003vra.3	-							NM_020911	NP_065962			plexin A4 isoform 1							integral to membrane|intracellular|plasma membrane				ovary(1)	1																		---	---	---	---
PLXNA4	91584	broad.mit.edu	37	7	132264198	132264199	+	5'Flank	DEL	GT	-	-	rs113591004		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132264198_132264199delGT	uc003vra.3	-						PLXNA4_uc003vrc.2_5'Flank|PLXNA4_uc003vrb.2_Intron	NM_020911	NP_065962			plexin A4 isoform 1							integral to membrane|intracellular|plasma membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	132391707	132391707	+	Intron	DEL	T	-	-	rs78786415		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132391707delT	uc003vrd.1	+											Homo sapiens cDNA FLJ40288 fis, clone TESTI2028098.																														---	---	---	---
CHCHD3	54927	broad.mit.edu	37	7	132602054	132602055	+	Intron	INS	-	A	A	rs11329832		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132602054_132602055insA	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	133514947	133514947	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133514947delT	uc003vrk.2	+						EXOC4_uc011kpo.1_Intron|EXOC4_uc003vrl.2_Intron|EXOC4_uc011kpp.1_Intron	NM_021807	NP_068579			SEC8 protein isoform a						vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			ovary(4)|large_intestine(3)|upper_aerodigestive_tract(1)|skin(1)	9		Esophageal squamous(399;0.129)																---	---	---	---
EXOC4	60412	broad.mit.edu	37	7	133615736	133615736	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133615736delT	uc003vrk.2	+						EXOC4_uc011kpo.1_Intron|EXOC4_uc003vrl.2_Intron|EXOC4_uc011kpp.1_Intron|EXOC4_uc011kpq.1_Intron	NM_021807	NP_068579			SEC8 protein isoform a						vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			ovary(4)|large_intestine(3)|upper_aerodigestive_tract(1)|skin(1)	9		Esophageal squamous(399;0.129)																---	---	---	---
Unknown	0	broad.mit.edu	37	7	134030114	134030114	+	IGR	DEL	T	-	-	rs71531819		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134030114delT								SLC35B4 (28287 upstream) : AKR1B1 (96993 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	134181655	134181655	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134181655delT								AKR1B1 (37767 upstream) : AKR1B10 (30689 downstream)																																			---	---	---	---
AGBL3	340351	broad.mit.edu	37	7	134805315	134805315	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134805315delT	uc011kpw.1	+						uc003vsg.2_Intron|C7orf49_uc003vsh.2_Intron	NM_178563	NP_848658			carboxypeptidase 3, cytosolic						proteolysis	cytosol	metallocarboxypeptidase activity|zinc ion binding				0																		---	---	---	---
WDR91	29062	broad.mit.edu	37	7	134880706	134880707	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134880706_134880707delAA	uc003vsp.2	-						WDR91_uc010lmq.2_Intron|WDR91_uc010lmr.2_Intron	NM_014149	NP_054868			WD repeat domain 91											breast(2)|ovary(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	135666884	135666884	+	IGR	DEL	A	-	-	rs77273486		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135666884delA								LUZP6 (4680 upstream) : CHRM2 (886515 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	136480679	136480679	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136480679delA								LUZP6 (818475 upstream) : CHRM2 (72720 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	136766124	136766124	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136766124delT	uc003vtp.1	-											Homo sapiens clone N1 NTera2D1 teratocarcinoma mRNA.																														---	---	---	---
DGKI	9162	broad.mit.edu	37	7	137165342	137165343	+	Intron	INS	-	T	T	rs71533752		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137165342_137165343insT	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	137337850	137337851	+	Intron	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137337850_137337851delGT	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	137463345	137463345	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137463345delA	uc003vtt.2	-						DGKI_uc003vtu.2_Intron	NM_004717	NP_004708			diacylglycerol kinase, iota						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	nucleus|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	137848125	137848125	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137848125delA								AKR1D1 (45075 upstream) : TRIM24 (296954 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	138004588	138004588	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138004588delA								AKR1D1 (201538 upstream) : TRIM24 (140491 downstream)																																			---	---	---	---
TTC26	79989	broad.mit.edu	37	7	138822525	138822525	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138822525delT	uc003vus.2	+						TTC26_uc003vuq.2_Intron|TTC26_uc011kqm.1_Intron|TTC26_uc003vur.3_Intron|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																		---	---	---	---
TTC26	79989	broad.mit.edu	37	7	138859787	138859787	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138859787delA	uc003vus.2	+						TTC26_uc011kqn.1_Intron|TTC26_uc011kqo.1_Intron|TTC26_uc011kqp.1_Intron|TTC26_uc003vut.2_Intron|TTC26_uc011kqq.1_Intron	NM_024926	NP_079202			tetratricopeptide repeat domain 26 isoform 1								binding			ovary(1)	1																		---	---	---	---
UBN2	254048	broad.mit.edu	37	7	138978319	138978321	+	Intron	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138978319_138978321delTTT	uc011kqr.1	+							NM_173569	NP_775840			ubinuclein 2											ovary(1)|skin(1)	2																		---	---	---	---
LUC7L2	51631	broad.mit.edu	37	7	139035428	139035428	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139035428delT	uc011kqt.1	+						LUC7L2_uc011kqs.1_Intron	NM_016019	NP_057103			LUC7-like 2								enzyme binding|metal ion binding				0	Melanoma(164;0.242)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	140145965	140145967	+	IGR	DEL	AAC	-	-	rs2030562	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140145965_140145967delAAC								RAB19 (19915 upstream) : MKRN1 (6873 downstream)																																			---	---	---	---
DENND2A	27147	broad.mit.edu	37	7	140309759	140309759	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140309759delT	uc010lnk.2	-						DENND2A_uc003vvw.2_Intron|DENND2A_uc003vvx.2_Intron	NM_015689	NP_056504			DENN/MADD domain containing 2A											ovary(3)|breast(1)	4	Melanoma(164;0.00956)																	---	---	---	---
DENND2A	27147	broad.mit.edu	37	7	140312918	140312918	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140312918delA	uc010lnk.2	-						DENND2A_uc003vvw.2_Intron|DENND2A_uc003vvx.2_Intron	NM_015689	NP_056504			DENN/MADD domain containing 2A											ovary(3)|breast(1)	4	Melanoma(164;0.00956)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	140349626	140349626	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140349626delA								DENND2A (8340 upstream) : ADCK2 (23327 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	140797594	140797598	+	IGR	DEL	TTTTT	-	-	rs72442379		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140797594_140797598delTTTTT								MRPS33 (82813 upstream) : AGK (453480 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	141119038	141119038	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141119038delA								MRPS33 (404257 upstream) : AGK (132040 downstream)																																			---	---	---	---
AGK	55750	broad.mit.edu	37	7	141272845	141272845	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141272845delT	uc003vwi.2	+						AGK_uc011krg.1_Intron|AGK_uc003vwh.2_Intron	NM_018238	NP_060708			acylglycerol kinase precursor						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway	mitochondrial membrane	acylglycerol kinase activity|ATP binding|diacylglycerol kinase activity|NAD+ kinase activity			ovary(1)|breast(1)	2	Melanoma(164;0.0171)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	141469761	141469762	+	IGR	INS	-	T	T	rs35776457		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141469761_141469762insT								TAS2R3 (4764 upstream) : TAS2R4 (8527 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	142147707	142147708	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142147707_142147708insT	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Intron					SubName: Full=V_segment translation product; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	142346809	142346809	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142346809delA	uc011krp.1	+						uc011krr.1_Intron|uc003vzp.2_Intron					Homo sapiens mRNA for T cell receptor beta variable 3, partial cds, clone: un 191.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	142685517	142685517	+	IGR	DEL	T	-	-	rs76201495		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142685517delT								KEL (26014 upstream) : OR9A2 (37770 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	142941903	142941903	+	IGR	DEL	A	-	-	rs79456015		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142941903delA								TAS2R40 (21761 upstream) : GSTK1 (18619 downstream)																																			---	---	---	---
ZYX	7791	broad.mit.edu	37	7	143083127	143083139	+	Intron	DEL	GTGTATGTGAGTG	-	-	rs113035029		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143083127_143083139delGTGTATGTGAGTG	uc003wcw.2	+						ZYX_uc011ktd.1_Intron|ZYX_uc003wcx.2_Intron|ZYX_uc011kte.1_Intron|ZYX_uc011ktf.1_Intron	NM_001010972	NP_001010972			zyxin						cell adhesion|cell-cell signaling|interspecies interaction between organisms|signal transduction	cell-cell adherens junction|cytoplasm|focal adhesion|integral to plasma membrane|nucleus|stress fiber	protein binding|zinc ion binding				0	Melanoma(164;0.205)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	143493856	143493856	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143493856delA	uc011ktn.1	+						uc011kto.1_Intron|uc011ktp.1_Intron|LOC154761_uc011ktq.1_Intron|LOC154761_uc011ktr.1_Intron|LOC154761_uc011kts.1_Intron|LOC154761_uc003wdj.1_Intron	NM_001130026	NP_001123498			hypothetical protein LOC285966 isoform B																														---	---	---	---
FAM115A	9747	broad.mit.edu	37	7	143591293	143591293	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143591293delA	uc003wdo.1	-						FAM115A_uc003wdp.1_Intron	NM_014719	NP_055534			hypothetical protein LOC9747												0	Melanoma(164;0.0903)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	143604876	143604876	+	IGR	DEL	T	-	-	rs113760276		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143604876delT								FAM115A (5657 upstream) : OR2F2 (27450 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	145553391	145553391	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145553391delA								None (None upstream) : CNTNAP2 (260062 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	145602771	145602774	+	IGR	DEL	AGAT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145602771_145602774delAGAT								None (None upstream) : CNTNAP2 (210679 downstream)																																			---	---	---	---
CNTNAP2	26047	broad.mit.edu	37	7	145813628	145813629	+	5'UTR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145813628_145813629delTT	uc003weu.1	+	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	146857030	146857030	+	Intron	DEL	T	-	-	rs35199333		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146857030delT	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	146880654	146880655	+	Intron	INS	-	GT	GT	rs146836693	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146880654_146880655insGT	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	146882124	146882124	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146882124delA	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	147034641	147034641	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147034641delA	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	147828942	147828942	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147828942delA	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	148051776	148051776	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148051776delT	uc003weu.1	+						CNTNAP2_uc003wev.1_Intron	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)			---	---	---	---
EZH2	2146	broad.mit.edu	37	7	148543931	148543936	+	Intron	DEL	TGTGTG	-	-	rs71884129	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148543931_148543936delTGTGTG	uc003wfd.1	-						EZH2_uc011kug.1_Intron|EZH2_uc003wfb.1_Intron|EZH2_uc003wfc.1_Intron|EZH2_uc011kuh.1_Intron|EZH2_uc011kui.1_Intron|EZH2_uc011kuj.1_Intron	NM_004456	NP_004447			enhancer of zeste 2 isoform a						negative regulation of retinoic acid receptor signaling pathway|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	DNA binding|histone-lysine N-methyltransferase activity|protein binding			haematopoietic_and_lymphoid_tissue(180)|skin(2)|large_intestine(1)	183	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)					Mis		DLBCL								---	---	---	---
Unknown	0	broad.mit.edu	37	7	148659301	148659301	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148659301delA								MIR1975 (20647 upstream) : PDIA4 (40853 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	149017661	149017661	+	IGR	DEL	T	-	-	rs77443212		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149017661delT								ZNF212 (64980 upstream) : ZNF777 (110800 downstream)																																			---	---	---	---
ZNF777	27153	broad.mit.edu	37	7	149136796	149136796	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149136796delA	uc003wfv.2	-							NM_015694	NP_056509			zinc finger protein 777						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	149890749	149890749	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149890749delT								ATP6V0E2 (312963 upstream) : ACTR3C (53553 downstream)																																			---	---	---	---
LOC100128542	100128542	broad.mit.edu	37	7	150482393	150482394	+	Intron	INS	-	T	T	rs141814107	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150482393_150482394insT	uc011kuw.1	+							NM_001162367	NP_001155839			hypothetical protein LOC100128542												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	150594622	150594622	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150594622delC								ABP1 (36243 upstream) : KCNH2 (47428 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	150607495	150607495	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150607495delT								ABP1 (49116 upstream) : KCNH2 (34555 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	152175478	152175478	+	IGR	DEL	T	-	-	rs77647563		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152175478delT								LOC100128822 (12850 upstream) : XRCC2 (168111 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	153157910	153157910	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153157910delA								ACTR3B (605447 upstream) : DPP6 (426509 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	153291592	153291592	+	IGR	DEL	A	-	-	rs114070122	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153291592delA								ACTR3B (739129 upstream) : DPP6 (292827 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	153505271	153505272	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153505271_153505272delTG								ACTR3B (952808 upstream) : DPP6 (79147 downstream)																																			---	---	---	---
DPP6	1804	broad.mit.edu	37	7	153870610	153870611	+	Intron	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153870610_153870611delCT	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.2_Intron	NM_130797	NP_570629			dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)															---	---	---	---
DPP6	1804	broad.mit.edu	37	7	153871959	153871960	+	Intron	INS	-	T	T	rs147664898	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153871959_153871960insT	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.2_Intron	NM_130797	NP_570629			dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)															---	---	---	---
DPP6	1804	broad.mit.edu	37	7	153987565	153987565	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153987565delC	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.2_Intron	NM_130797	NP_570629			dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)															---	---	---	---
DPP6	1804	broad.mit.edu	37	7	154432667	154432667	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154432667delT	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlm.2_Intron|DPP6_uc011kvq.1_Intron	NM_130797	NP_570629			dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)															---	---	---	---
DPP6	1804	broad.mit.edu	37	7	154543550	154543550	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154543550delG	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	154687276	154687277	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154687276_154687277delTT								DPP6 (1282 upstream) : LOC100132707 (32950 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	154841688	154841688	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154841688delT								LOC202781 (44276 upstream) : HTR5A (20858 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	155817922	155817923	+	IGR	INS	-	TG	TG	rs151259073	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155817922_155817923insTG								SHH (212955 upstream) : C7orf4 (515262 downstream)																																			---	---	---	---
PTPRN2	5799	broad.mit.edu	37	7	157338027	157338027	+	Intron	DEL	T	-	-	rs113095456	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157338027delT	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron|PTPRN2_uc003wnn.2_Intron	NM_002847	NP_002838			protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)														---	---	---	---
PTPRN2	5799	broad.mit.edu	37	7	157445294	157445294	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157445294delG	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	158353998	158353999	+	Intron	DEL	CC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158353998_158353999delCC	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.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)														---	---	---	---
NCAPG2	54892	broad.mit.edu	37	7	158429647	158429648	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158429647_158429648insT	uc003wnv.1	-						NCAPG2_uc010lqu.1_Intron|NCAPG2_uc003wnw.1_Intron|NCAPG2_uc003wnx.1_Intron|NCAPG2_uc011kwc.1_Intron	NM_017760	NP_060230			leucine zipper protein 5						cell division|chromosome condensation|mitosis	nucleus	methylated histone residue binding			ovary(1)|breast(1)|kidney(1)	3	Ovarian(565;0.152)	all_cancers(7;3.44e-11)|all_epithelial(9;3.05e-05)|all_hematologic(28;0.014)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.187)|STAD - Stomach adenocarcinoma(7;0.18)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	158509788	158509790	+	IGR	DEL	TCC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158509788_158509790delTCC								NCAPG2 (12268 upstream) : ESYT2 (13899 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	158509957	158509959	+	IGR	DEL	CTT	-	-	rs138946201	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158509957_158509959delCTT								NCAPG2 (12437 upstream) : ESYT2 (13730 downstream)																																			---	---	---	---
ESYT2	57488	broad.mit.edu	37	7	158585768	158585769	+	Intron	INS	-	AAC	AAC	rs148505845	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158585768_158585769insAAC	uc003wob.1	-						ESYT2_uc003woc.1_Intron|ESYT2_uc003wod.1_Intron	NM_020728	NP_065779			family with sequence similarity 62 (C2 domain							integral to membrane|plasma membrane				central_nervous_system(2)|kidney(1)	3																		---	---	---	---
WDR60	55112	broad.mit.edu	37	7	158678037	158678038	+	Intron	DEL	TT	-	-	rs72451610		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158678037_158678038delTT	uc003woe.3	+						WDR60_uc010lqv.2_Intron|WDR60_uc010lqw.2_Intron	NM_018051	NP_060521			WD repeat domain 60											ovary(2)|breast(1)|central_nervous_system(1)	4	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)														---	---	---	---
FBXO25	26260	broad.mit.edu	37	8	363407	363407	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:363407delT	uc003wox.2	+						FBXO25_uc003woy.2_Intron|FBXO25_uc003woz.2_Intron	NM_183421	NP_904357			F-box only protein 25 isoform 1							nucleus|SCF ubiquitin ligase complex	actin binding|ubiquitin-protein ligase activity			lung(1)	1		Ovarian(12;0.00965)|Colorectal(14;0.0815)|Myeloproliferative disorder(644;0.116)|all_neural(12;0.122)		Epithelial(5;3.14e-14)|OV - Ovarian serous cystadenocarcinoma(5;1.56e-07)|BRCA - Breast invasive adenocarcinoma(11;1.88e-06)														---	---	---	---
C8orf42	157695	broad.mit.edu	37	8	444131	444132	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:444131_444132delTT	uc003wpd.2	-						C8orf42_uc011kwg.1_Intron	NM_175075	NP_778250			hypothetical protein LOC157695												0		Ovarian(12;0.0481)|Colorectal(14;0.0815)|Hepatocellular(245;0.0968)|Myeloproliferative disorder(644;0.116)|all_neural(12;0.122)		Epithelial(5;5.16e-14)|OV - Ovarian serous cystadenocarcinoma(5;7.35e-07)|BRCA - Breast invasive adenocarcinoma(11;4.17e-06)|COAD - Colon adenocarcinoma(149;0.0255)														---	---	---	---
C8orf42	157695	broad.mit.edu	37	8	463111	463111	+	Intron	DEL	A	-	-	rs151241976		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:463111delA	uc003wpd.2	-						C8orf42_uc011kwg.1_Intron	NM_175075	NP_778250			hypothetical protein LOC157695												0		Ovarian(12;0.0481)|Colorectal(14;0.0815)|Hepatocellular(245;0.0968)|Myeloproliferative disorder(644;0.116)|all_neural(12;0.122)		Epithelial(5;5.16e-14)|OV - Ovarian serous cystadenocarcinoma(5;7.35e-07)|BRCA - Breast invasive adenocarcinoma(11;4.17e-06)|COAD - Colon adenocarcinoma(149;0.0255)														---	---	---	---
ERICH1	157697	broad.mit.edu	37	8	616363	616363	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:616363delT	uc003wph.2	-						ERICH1_uc011kwh.1_Intron|ERICH1_uc003wpe.1_Intron|ERICH1_uc003wpi.2_3'UTR	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	823711	823711	+	Intron	DEL	T	-	-	rs982351	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:823711delT	uc003wpj.1	+											Homo sapiens cDNA clone IMAGE:4824304.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	1097259	1097259	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1097259delA								ERICH1 (416033 upstream) : DLGAP2 (352310 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	1259214	1259214	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1259214delA								ERICH1 (577988 upstream) : DLGAP2 (190355 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	1442893	1442893	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1442893delA								ERICH1 (761667 upstream) : DLGAP2 (6676 downstream)																																			---	---	---	---
DLGAP2	9228	broad.mit.edu	37	8	1449924	1449924	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1449924delG	uc003wpl.2	+							NM_004745	NP_004736			discs large-associated protein 2						neuron-neuron synaptic transmission	cell junction|neurofilament|postsynaptic density|postsynaptic membrane	protein binding				0		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)														---	---	---	---
ARHGEF10	9639	broad.mit.edu	37	8	1817227	1817227	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1817227delA	uc003wpr.2	+						ARHGEF10_uc003wpq.1_Intron|ARHGEF10_uc003wps.2_Intron|ARHGEF10_uc003wpt.2_Intron|ARHGEF10_uc010lrd.1_Intron|ARHGEF10_uc003wpu.2_Intron	NM_014629	NP_055444			Rho guanine nucleotide exchange factor 10						centrosome duplication|myelination in peripheral nervous system|positive regulation of GTP catabolic process|positive regulation of stress fiber assembly|regulation of Rho protein signal transduction|spindle assembly involved in mitosis	centrosome|cytosol|soluble fraction	kinesin binding|Rho guanyl-nucleotide exchange factor activity			large_intestine(1)	1		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	2474406	2474407	+	Intron	INS	-	CTCA	CTCA	rs151263131	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2474406_2474407insCTCA	uc003wqa.2	-											Homo sapiens cDNA clone IMAGE:4830065.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	2518978	2518978	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2518978delT								MYOM2 (425599 upstream) : CSMD1 (273898 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	2578661	2578661	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2578661delT	uc003wqb.1	-											Homo sapiens cDNA FLJ46912 fis, clone SKNMC2000583.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	2718540	2718540	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2718540delA								MYOM2 (625161 upstream) : CSMD1 (74336 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	2777200	2777203	+	IGR	DEL	TTCC	-	-	rs113064400		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2777200_2777203delTTCC								MYOM2 (683821 upstream) : CSMD1 (15673 downstream)																																			---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	2821034	2821034	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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	3219587	3219587	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3219587delT	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	3439320	3439320	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3439320delT	uc011kwk.1	-							NM_033225	NP_150094			CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)														---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	3593936	3593936	+	Intron	DEL	A	-	-	rs34615106		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3593936delA	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	3900495	3900495	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3900495delA	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	3935527	3935527	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3935527delA	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	4165766	4165766	+	Intron	DEL	T	-	-	rs138912919	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4165766delT	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	4212847	4212848	+	Intron	INS	-	CA	CA	rs142698665	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4212847_4212848insCA	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	4382092	4382094	+	Intron	DEL	TTT	-	-	rs148248967		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4382092_4382094delTTT	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	4673715	4673716	+	Intron	INS	-	T	T	rs140905000	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4673715_4673716insT	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	4700956	4700957	+	Intron	INS	-	ACA	ACA	rs141163330	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4700956_4700957insACA	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	4913805	4913805	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4913805delA								CSMD1 (61477 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	6210596	6210597	+	IGR	INS	-	G	G	rs139479187	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6210596_6210597insG								None (None upstream) : MCPH1 (53524 downstream)																																			---	---	---	---
MCPH1	79648	broad.mit.edu	37	8	6383956	6383956	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6383956delA	uc003wqi.2	+						ANGPT2_uc003wqj.3_Intron|ANGPT2_uc003wqk.3_Intron|ANGPT2_uc010lri.2_Intron|ANGPT2_uc003wql.3_Intron	NM_024596	NP_078872			microcephalin							microtubule organizing center				central_nervous_system(1)|skin(1)	2		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)														---	---	---	---
MCPH1	79648	broad.mit.edu	37	8	6408751	6408751	+	Intron	DEL	T	-	-	rs34057336		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6408751delT	uc003wqi.2	+						ANGPT2_uc003wqj.3_Intron|ANGPT2_uc003wqk.3_Intron|ANGPT2_uc010lri.2_Intron|ANGPT2_uc003wql.3_Intron	NM_024596	NP_078872			microcephalin							microtubule organizing center				central_nervous_system(1)|skin(1)	2		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)														---	---	---	---
AGPAT5	55326	broad.mit.edu	37	8	6591790	6591792	+	Intron	DEL	ATT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6591790_6591792delATT	uc003wqo.2	+						AGPAT5_uc011kwm.1_Intron	NM_018361	NP_060831			1-acylglycerol-3-phosphate O-acyltransferase 5						phospholipid biosynthetic process	integral to membrane|mitochondrion	1-acylglycerol-3-phosphate O-acyltransferase activity				0			STAD - Stomach adenocarcinoma(24;0.0578)	READ - Rectum adenocarcinoma(644;0.156)|COAD - Colon adenocarcinoma(149;0.191)														---	---	---	---
DEFB1	1672	broad.mit.edu	37	8	6728885	6728886	+	Intron	INS	-	T	T	rs1344197	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6728885_6728886insT	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)														---	---	---	---
LOC349196	349196	broad.mit.edu	37	8	7196263	7196264	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:7196263_7196264delAC	uc010lrk.1	-						uc011kwo.1_Intron					Homo sapiens cDNA FLJ37516 fis, clone BRCAN2000832.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	7274111	7274111	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:7274111delA								LOC349196 (61237 upstream) : DEFB103B (12380 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	7768419	7768420	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:7768419_7768420delAA								DEFB4A (14183 upstream) : FAM66E (44115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	7992648	7992648	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:7992648delC								MIR548I3 (46037 upstream) : FLJ10661 (93444 downstream)																																			---	---	---	---
SGK223	157285	broad.mit.edu	37	8	8182382	8182382	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8182382delT	uc003wsh.3	-							NM_001080826	NP_001074295			pragmin								ATP binding|non-membrane spanning protein tyrosine kinase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	8978196	8978197	+	IGR	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8978196_8978197delGT								ERI1 (87347 upstream) : PPP1R3B (15577 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	9074194	9074194	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9074194delC								PPP1R3B (65110 upstream) : TNKS (339251 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	9242991	9242991	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9242991delA								PPP1R3B (233907 upstream) : TNKS (170454 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	9385721	9385721	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9385721delA								PPP1R3B (376637 upstream) : TNKS (27724 downstream)																																			---	---	---	---
TNKS	8658	broad.mit.edu	37	8	9481652	9481652	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9481652delA	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)														---	---	---	---
TNKS	8658	broad.mit.edu	37	8	9629311	9629312	+	Intron	INS	-	AGG	AGG	rs137940834	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9629311_9629312insAGG	uc003wss.2	+						TNKS_uc011kww.1_Intron	NM_003747	NP_003738			tankyrase, TRF1-interacting ankyrin-related						mitotic spindle organization|mRNA transport|negative regulation of DNA binding|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of telomere maintenance via telomerase|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein poly-ADP-ribosylation|protein polyubiquitination|protein transport|spindle assembly|transmembrane transport|Wnt receptor signaling pathway	chromosome, centromeric region|Golgi membrane|microsome|nuclear chromosome, telomeric region|nuclear membrane|nuclear pore|pericentriolar material	NAD+ ADP-ribosyltransferase activity|protein binding|zinc ion binding			lung(4)|ovary(2)|kidney(1)	7				COAD - Colon adenocarcinoma(149;0.0467)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	9685070	9685071	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9685070_9685071delAA								TNKS (45215 upstream) : LOC157627 (72503 downstream)																																			---	---	---	---
MSRA	4482	broad.mit.edu	37	8	9926277	9926277	+	Intron	DEL	C	-	-	rs73189199	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9926277delC	uc003wsx.2	+						MSRA_uc011kwx.1_Intron	NM_012331	NP_036463			methionine sulfoxide reductase A isoform a						methionine metabolic process|protein modification process|response to oxidative stress	mitochondrion|nucleus	peptide-methionine-(S)-S-oxide reductase activity				0		Myeloproliferative disorder(644;0.178)			L-Methionine(DB00134)													---	---	---	---
MSRA	4482	broad.mit.edu	37	8	10118205	10118206	+	Intron	INS	-	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10118205_10118206insG	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	10332691	10332691	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10332691delT								MSRA (46292 upstream) : PRSS55 (50390 downstream)																																			---	---	---	---
SOX7	83595	broad.mit.edu	37	8	10601488	10601488	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10601488delA	uc011kwz.1	-						uc003wtg.1_Intron	NM_031439	NP_113627			SRY-box 7						endoderm formation|negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|positive regulation of caspase activity|regulation of canonical Wnt receptor signaling pathway	cytoplasm|nucleus	transcription regulatory region DNA binding			breast(1)	1				COAD - Colon adenocarcinoma(149;0.0732)														---	---	---	---
SOX7	83595	broad.mit.edu	37	8	10650966	10650966	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10650966delA	uc011kwz.1	-						PINX1_uc003wth.2_Intron|PINX1_uc003wti.2_Intron	NM_031439	NP_113627			SRY-box 7						endoderm formation|negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|positive regulation of caspase activity|regulation of canonical Wnt receptor signaling pathway	cytoplasm|nucleus	transcription regulatory region DNA binding			breast(1)	1				COAD - Colon adenocarcinoma(149;0.0732)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	10702394	10702394	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10702394delT								SOX7 (5095 upstream) : XKR6 (51263 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	10717220	10717220	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10717220delT	uc003wtj.2	-											Homo sapiens cDNA FLJ37206 fis, clone BRALZ2007545.																														---	---	---	---
XKR6	286046	broad.mit.edu	37	8	10754927	10754927	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10754927delA	uc003wtk.1	-	3						NM_173683	NP_775954			XK, Kell blood group complex subunit-related							integral to membrane				ovary(1)|skin(1)	2				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)														---	---	---	---
XKR6	286046	broad.mit.edu	37	8	10843168	10843168	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10843168delA	uc003wtk.1	-							NM_173683	NP_775954			XK, Kell blood group complex subunit-related							integral to membrane				ovary(1)|skin(1)	2				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)														---	---	---	---
FAM167A	83648	broad.mit.edu	37	8	11316295	11316295	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11316295delA	uc003wtw.2	-							NM_053279	NP_444509			hypothetical protein LOC83648												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	11506698	11506699	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11506698_11506699delAA								BLK (84591 upstream) : GATA4 (27769 downstream)																																			---	---	---	---
NEIL2	252969	broad.mit.edu	37	8	11626906	11626906	+	5'Flank	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11626906delA	uc003wug.2	+						NEIL2_uc003wue.2_5'Flank|NEIL2_uc003wuf.2_5'Flank|NEIL2_uc011kxd.1_5'Flank	NM_145043	NP_659480			nei like 2 isoform a						base-excision repair|nucleotide-excision repair	nucleus	damaged DNA binding|DNA-(apurinic or apyrimidinic site) lyase activity|hydrolase activity, hydrolyzing N-glycosyl compounds|zinc ion binding				0	all_epithelial(15;0.103)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.166)									BER_DNA_glycosylases					---	---	---	---
FDFT1	2222	broad.mit.edu	37	8	11685629	11685629	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11685629delA	uc003wui.2	+						FDFT1_uc003wuh.2_Intron|FDFT1_uc010lsa.1_Intron|FDFT1_uc011kxe.1_Intron|FDFT1_uc011kxf.1_Intron|FDFT1_uc011kxg.1_Intron|FDFT1_uc003wuj.2_Intron|FDFT1_uc010lsb.2_Intron|FDFT1_uc011kxh.1_Intron|FDFT1_uc011kxi.1_Intron|FDFT1_uc011kxj.1_Intron|FDFT1_uc003wuk.2_Intron|FDFT1_uc011kxk.1_Intron	NM_004462	NP_004453			squalene synthase						cholesterol biosynthetic process|isoprenoid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	farnesyl-diphosphate farnesyltransferase activity|oxidoreductase activity|protein binding|squalene synthase activity				0	all_epithelial(15;0.234)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.18)														---	---	---	---
FAM66D	100132923	broad.mit.edu	37	8	11996683	11996684	+	Intron	INS	-	TC	TC	rs143497277	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11996683_11996684insTC	uc011kxo.1	+						FAM66D_uc011kxp.1_Intron|USP17L2_uc003wvc.1_5'Flank	NR_027425				Homo sapiens cDNA FLJ56781 complete cds.												0																		---	---	---	---
FAM66D	100132923	broad.mit.edu	37	8	12002444	12002445	+	Intron	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12002444_12002445delTG	uc011kxo.1	+						FAM66D_uc011kxp.1_Intron	NR_027425				Homo sapiens cDNA FLJ56781 complete cds.												0																		---	---	---	---
FAM66D	100132923	broad.mit.edu	37	8	12401082	12401082	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12401082delG	uc011kxp.1	+						uc003wvm.1_Intron|uc003wvv.2_Intron|uc003wvw.1_Intron|uc003wvx.1_Intron|uc003wvy.3_Intron					Homo sapiens cDNA FLJ37098 fis, clone BRACE2019004.												0																		---	---	---	---
SGCZ	137868	broad.mit.edu	37	8	14079475	14079475	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14079475delA	uc003wwq.2	-						SGCZ_uc010lss.2_Intron	NM_139167	NP_631906			sarcoglycan zeta						cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)														---	---	---	---
SGCZ	137868	broad.mit.edu	37	8	14167359	14167359	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14167359delT	uc003wwq.2	-						SGCZ_uc010lss.2_Intron	NM_139167	NP_631906			sarcoglycan zeta						cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)														---	---	---	---
SGCZ	137868	broad.mit.edu	37	8	14210583	14210608	+	Intron	DEL	CATGAGTTTGAAATCTTGTTCTTACA	-	-	rs67374918		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14210583_14210608delCATGAGTTTGAAATCTTGTTCTTACA	uc003wwq.2	-						SGCZ_uc010lss.2_Intron	NM_139167	NP_631906			sarcoglycan zeta						cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)														---	---	---	---
SGCZ	137868	broad.mit.edu	37	8	14221047	14221047	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14221047delT	uc003wwq.2	-						SGCZ_uc010lss.2_Intron	NM_139167	NP_631906			sarcoglycan zeta						cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)														---	---	---	---
SGCZ	137868	broad.mit.edu	37	8	14643419	14643419	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14643419delT	uc003wwq.2	-							NM_139167	NP_631906			sarcoglycan zeta						cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)														---	---	---	---
TUSC3	7991	broad.mit.edu	37	8	15593380	15593380	+	Intron	DEL	T	-	-	rs73197178		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15593380delT	uc003wwt.2	+						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)														---	---	---	---
MTMR7	9108	broad.mit.edu	37	8	17219046	17219046	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17219046delT	uc003wxm.2	-							NM_004686	NP_004677			myotubularin related protein 7								protein tyrosine phosphatase activity			skin(1)	1				Colorectal(111;0.112)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	17304481	17304482	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17304481_17304482insA								MTMR7 (33441 upstream) : SLC7A2 (50118 downstream)																																			---	---	---	---
SLC7A2	6542	broad.mit.edu	37	8	17385441	17385441	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17385441delT	uc011kyc.1	+							NM_001008539	NP_001008539			solute carrier family 7, member 2 isoform 2						cellular amino acid metabolic process|ion transport	cytoplasm|integral to plasma membrane|membrane fraction	basic amino acid transmembrane transporter activity			ovary(2)|skin(1)	3				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	L-Lysine(DB00123)|L-Ornithine(DB00129)													---	---	---	---
MTUS1	57509	broad.mit.edu	37	8	17581721	17581721	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17581721delA	uc003wxv.2	-						MTUS1_uc003wxt.2_5'Flank|MTUS1_uc011kyg.1_5'Flank|MTUS1_uc010lsy.2_Intron|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)														---	---	---	---
PSD3	23362	broad.mit.edu	37	8	18605325	18605325	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18605325delA	uc003wza.2	-						PSD3_uc003wyy.2_Intron|PSD3_uc003wyz.2_Intron	NM_015310	NP_056125			ADP-ribosylation factor guanine nucleotide						regulation of ARF protein signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	ARF guanyl-nucleotide exchange factor activity			ovary(3)	3				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	19003734	19003734	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19003734delA								PSD3 (132538 upstream) : SH2D4A (167473 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	19031137	19031137	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19031137delT								PSD3 (159941 upstream) : SH2D4A (140070 downstream)																																			---	---	---	---
SH2D4A	63898	broad.mit.edu	37	8	19177406	19177407	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19177406_19177407delAC	uc003wzb.2	+						SH2D4A_uc011kym.1_Intron|SH2D4A_uc003wzc.2_Intron	NM_022071	NP_071354			SH2 domain containing 4A							cytoplasm|nucleus	protein binding				0				Colorectal(111;0.0732)														---	---	---	---
CSGALNACT1	55790	broad.mit.edu	37	8	19320325	19320325	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19320325delT	uc011kyn.1	-						CSGALNACT1_uc011kyo.1_Intron|CSGALNACT1_uc003wzg.2_Intron|CSGALNACT1_uc011kyp.1_Intron|CSGALNACT1_uc003wzh.2_Intron	NM_001130518	NP_001123990			chondroitin sulfate						anatomical structure morphogenesis|cell proliferation|cell recognition|chondroitin sulfate biosynthetic process|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|dermatan sulfate proteoglycan biosynthetic process|extracellular matrix organization|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|heparin biosynthetic process|nervous system development|UDP-glucuronate metabolic process|UDP-N-acetylgalactosamine metabolic process	Golgi cisterna membrane|integral to Golgi membrane|soluble fraction	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|glucuronosyltransferase activity|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|peptidoglycan glycosyltransferase activity			central_nervous_system(2)|ovary(1)	3				Colorectal(111;0.182)														---	---	---	---
CSGALNACT1	55790	broad.mit.edu	37	8	19414201	19414201	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19414201delT	uc011kyn.1	-						CSGALNACT1_uc011kyo.1_Intron|CSGALNACT1_uc003wzg.2_Intron|CSGALNACT1_uc011kyp.1_Intron|CSGALNACT1_uc003wzh.2_Intron	NM_001130518	NP_001123990			chondroitin sulfate						anatomical structure morphogenesis|cell proliferation|cell recognition|chondroitin sulfate biosynthetic process|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|dermatan sulfate proteoglycan biosynthetic process|extracellular matrix organization|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|heparin biosynthetic process|nervous system development|UDP-glucuronate metabolic process|UDP-N-acetylgalactosamine metabolic process	Golgi cisterna membrane|integral to Golgi membrane|soluble fraction	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|glucuronosyltransferase activity|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|peptidoglycan glycosyltransferase activity			central_nervous_system(2)|ovary(1)	3				Colorectal(111;0.182)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	20139083	20139083	+	IGR	DEL	A	-	-	rs75501281		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20139083delA								LZTS1 (26280 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	20169119	20169120	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20169119_20169120delTC								LZTS1 (56316 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	20644025	20644026	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20644025_20644026delAA								LZTS1 (531222 upstream) : GFRA2 (905504 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21004273	21004273	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21004273delT								LZTS1 (891470 upstream) : GFRA2 (545257 downstream)																																			---	---	---	---
BMP1	649	broad.mit.edu	37	8	22029576	22029577	+	Intron	INS	-	GT	GT	rs148107356	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22029576_22029577insGT	uc003xbg.2	+						BMP1_uc011kzb.1_Intron|BMP1_uc003xba.2_Intron|BMP1_uc003xbb.2_Intron|BMP1_uc003xbe.2_Intron|BMP1_uc003xbc.2_Intron|BMP1_uc003xbd.2_Intron|BMP1_uc003xbf.2_Intron|BMP1_uc011kzc.1_Intron|BMP1_uc003xbh.2_Intron|BMP1_uc003xbi.2_Intron	NM_006129	NP_006120			bone morphogenetic protein 1 isoform 3						cartilage condensation|cell differentiation|lipid metabolic process|lipoprotein metabolic process|ossification|positive regulation of cartilage development|proteolysis	extracellular space	calcium ion binding|cytokine activity|growth factor activity|metalloendopeptidase activity|zinc ion binding			ovary(2)|breast(1)	3				Colorectal(74;0.00229)|COAD - Colon adenocarcinoma(73;0.0661)|READ - Rectum adenocarcinoma(644;0.11)														---	---	---	---
PPP3CC	5533	broad.mit.edu	37	8	22382671	22382671	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22382671delA	uc003xbs.2	+						PPP3CC_uc011kzi.1_Intron|PPP3CC_uc003xbt.2_Intron|PPP3CC_uc011kzj.1_Intron	NM_005605	NP_005596			protein phosphatase 3, catalytic subunit, gamma						activation of pro-apoptotic gene products|induction of apoptosis by intracellular signals	cytosol	calmodulin binding|metal ion binding|phosphoprotein phosphatase activity			ovary(1)	1		Prostate(55;0.104)		BRCA - Breast invasive adenocarcinoma(99;0.00756)|Colorectal(74;0.0238)|COAD - Colon adenocarcinoma(73;0.0835)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	22562173	22562174	+	IGR	DEL	AA	-	-	rs112421503		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22562173_22562174delAA								EGR3 (11358 upstream) : PEBP4 (8591 downstream)																																	OREG0018619	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PEBP4	157310	broad.mit.edu	37	8	22694401	22694402	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22694401_22694402delAA	uc003xcn.1	-							NM_144962	NP_659399			phosphatidylethanolamine-binding protein 4							lysosome				ovary(1)|large_intestine(1)|breast(1)|skin(1)	4		Prostate(55;0.0453)|Breast(100;0.103)		Colorectal(74;0.0434)|COAD - Colon adenocarcinoma(73;0.124)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	23126436	23126437	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23126436_23126437delAC								CHMP7 (6924 upstream) : R3HCC1 (19175 downstream)																																			---	---	---	---
LOXL2	4017	broad.mit.edu	37	8	23253865	23253865	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23253865delA	uc003xdh.1	-						ENTPD4_uc011kzu.1_Intron	NM_002318	NP_002309			lysyl oxidase-like 2 precursor						aging|cell adhesion|protein modification process	extracellular space|membrane	copper ion binding|electron carrier activity|oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor|scavenger receptor activity			breast(2)|ovary(1)	3		Prostate(55;0.0453)|Breast(100;0.143)		Colorectal(74;0.0288)|COAD - Colon adenocarcinoma(73;0.096)														---	---	---	---
STC1	6781	broad.mit.edu	37	8	23709570	23709571	+	Intron	DEL	TG	-	-	rs113294965		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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	23770031	23770032	+	IGR	DEL	TG	-	-	rs71549824		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23770031_23770032delTG								STC1 (57711 upstream) : ADAM28 (381548 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	23827628	23827628	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23827628delA								STC1 (115308 upstream) : ADAM28 (323952 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	23890133	23890133	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23890133delT								STC1 (177813 upstream) : ADAM28 (261447 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	23978935	23978935	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23978935delG								STC1 (266615 upstream) : ADAM28 (172645 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	24124464	24124465	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24124464_24124465delAA								STC1 (412144 upstream) : ADAM28 (27115 downstream)																																			---	---	---	---
ADAM7	8756	broad.mit.edu	37	8	24315378	24315379	+	Intron	INS	-	GTGTGA	GTGTGA	rs151208323	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24315378_24315379insGTGTGA	uc003xeb.2	+						ADAM7_uc003xea.1_Intron	NM_003817	NP_003808			a disintegrin and metalloproteinase domain 7						proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			skin(3)|ovary(1)|kidney(1)	5		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	24781443	24781443	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24781443delG								NEFM (4838 upstream) : NEFL (27028 downstream)																																			---	---	---	---
DOCK5	80005	broad.mit.edu	37	8	25268496	25268505	+	Intron	DEL	CGCGCACGCA	-	-	rs75357757	by1000genomes;by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25268496_25268505delCGCGCACGCA	uc003xeg.2	+						PPP2R2A_uc003xek.2_Intron|DOCK5_uc003xej.2_Intron	NM_024940	NP_079216			dedicator of cytokinesis 5							cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)	3		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)														---	---	---	---
EBF2	64641	broad.mit.edu	37	8	25708397	25708397	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25708397delA	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	25761243	25761243	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25761243delA	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	26019751	26019753	+	Intron	DEL	TTT	-	-	rs12114517	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26019751_26019753delTTT	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	26035779	26035779	+	Intron	DEL	A	-	-	rs80233202		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26035779delA	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	26063940	26063941	+	Intron	DEL	CA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26063940_26063941delCA	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	26170560	26170560	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26170560delT	uc003xeu.2	+						PPP2R2A_uc003xek.2_Intron|PPP2R2A_uc011laf.1_Intron	NM_002717	NP_002708			alpha isoform of regulatory subunit B55, protein						protein dephosphorylation|signal transduction	protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity|protein serine/threonine phosphatase activity			ovary(1)|kidney(1)	2		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)														---	---	---	---
DPYSL2	1808	broad.mit.edu	37	8	26381172	26381172	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26381172delT	uc003xfa.2	+							NM_001386	NP_001377			dihydropyrimidinase-like 2						axon guidance|pyrimidine base catabolic process|signal transduction	cytosol	dihydropyrimidinase activity|protein binding			large_intestine(1)	1		all_cancers(63;0.121)|Ovarian(32;2.68e-05)|all_epithelial(46;0.116)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;3.33e-10)|Colorectal(74;0.183)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	26532275	26532275	+	IGR	DEL	T	-	-	rs55828531	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26532275delT								DPYSL2 (16582 upstream) : ADRA1A (73392 downstream)																																			---	---	---	---
EPHX2	2053	broad.mit.edu	37	8	27358903	27358904	+	Intron	DEL	TC	-	-	rs71220598		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27358903_27358904delTC	uc003xfu.2	+						EPHX2_uc010lut.1_Intron|EPHX2_uc010luu.2_Intron|EPHX2_uc010luv.2_Intron|EPHX2_uc003xfv.2_Intron|EPHX2_uc010luw.2_Intron	NM_001979	NP_001970			epoxide hydrolase 2, cytoplasmic						aromatic compound catabolic process|cellular calcium ion homeostasis|drug metabolic process|inflammatory response|positive regulation of vasodilation|reactive oxygen species metabolic process|regulation of blood pressure|response to toxin|xenobiotic metabolic process	cytosol|focal adhesion|Golgi apparatus|nucleolus|peroxisome|soluble fraction	epoxide hydrolase activity|metal ion binding|protein homodimerization activity			ovary(1)	1		Ovarian(32;2.61e-05)|all_epithelial(46;0.207)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0226)|Epithelial(17;1.12e-09)|Colorectal(74;0.157)	Tamoxifen(DB00675)													---	---	---	---
SCARA3	51435	broad.mit.edu	37	8	27512118	27512119	+	Intron	INS	-	A	A	rs144109617	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27512118_27512119insA	uc003xga.1	+						SCARA3_uc003xgb.1_Intron	NM_016240	NP_057324			scavenger receptor class A, member 3 isoform 1						response to oxidative stress|UV protection	collagen|endoplasmic reticulum membrane|Golgi membrane|integral to membrane	scavenger receptor activity			skin(2)|ovary(1)|breast(1)	4		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0219)|Colorectal(74;0.148)														---	---	---	---
ELP3	55140	broad.mit.edu	37	8	27975250	27975250	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27975250delA	uc003xgo.3	+						ELP3_uc003xgn.3_Intron|ELP3_uc011laq.1_Intron|ELP3_uc011lar.1_Intron|ELP3_uc011las.1_Intron|ELP3_uc011lat.1_Intron	NM_018091	NP_060561			elongation protein 3 homolog						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|DNA-directed RNA polymerase II, holoenzyme|nucleolus|transcription elongation factor complex	histone acetyltransferase activity|iron-sulfur cluster binding|metal ion binding|phosphorylase kinase regulator activity|protein binding				0		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.151)|Colorectal(74;0.183)														---	---	---	---
ZNF395	55893	broad.mit.edu	37	8	28312760	28312761	+	Intron	DEL	TT	-	-	rs112832862		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28312760_28312761delTT	uc003xgt.2	-						FBXO16_uc003xgu.2_Intron|FBXO16_uc003xgv.2_Intron|FBXO16_uc003xgw.2_Intron	NM_018660	NP_061130			zinc finger protein 395						transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding				0		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.102)|Kidney(114;0.123)|Colorectal(74;0.142)														---	---	---	---
ZNF395	55893	broad.mit.edu	37	8	28338020	28338020	+	Intron	DEL	T	-	-	rs74663473		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28338020delT	uc003xgt.2	-						FBXO16_uc003xgu.2_Intron|FBXO16_uc003xgv.2_Intron|FBXO16_uc003xgw.2_Intron	NM_018660	NP_061130			zinc finger protein 395						transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding				0		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.102)|Kidney(114;0.123)|Colorectal(74;0.142)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	28436921	28436921	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28436921delA								FZD3 (14962 upstream) : EXTL3 (122232 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	29364797	29364797	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29364797delT								DUSP4 (156612 upstream) : C8orf75 (213981 downstream)																																			---	---	---	---
LOC286135	286135	broad.mit.edu	37	8	29797302	29797302	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29797302delA	uc003xhq.3	+							NR_024473				Homo sapiens mRNA; cDNA DKFZp686I2037 (from clone DKFZp686I2037).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	29847328	29847328	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29847328delA								LOC286135 (36207 upstream) : TMEM66 (73304 downstream)																																			---	---	---	---
LEPROTL1	23484	broad.mit.edu	37	8	29959560	29959560	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29959560delT	uc003xhw.3	+						LEPROTL1_uc003xhx.2_Intron	NM_015344	NP_056159			leptin receptor overlapping transcript-like 1							integral to membrane					0				KIRC - Kidney renal clear cell carcinoma(542;0.094)|Kidney(114;0.113)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	30181795	30181802	+	IGR	DEL	AGAAAGGG	-	-	rs72142959		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30181795_30181802delAGAAAGGG								DCTN6 (140736 upstream) : RBPMS (60142 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	30192416	30192416	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30192416delT								DCTN6 (151357 upstream) : RBPMS (49528 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	30227053	30227054	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30227053_30227054delAA								DCTN6 (185994 upstream) : RBPMS (14890 downstream)																																			---	---	---	---
RBPMS	11030	broad.mit.edu	37	8	30407259	30407260	+	Intron	INS	-	TTTCTTTGCT	TTTCTTTGCT	rs139991132	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30407259_30407260insTTTCTTTGCT	uc003xic.1	+						RBPMS_uc003xid.1_Intron|RBPMS_uc003xie.1_Intron|RBPMS_uc003xif.1_Intron	NM_006867	NP_006858			RNA-binding protein with multiple splicing						positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|regulation of transcription, DNA-dependent|RNA processing|transcription, DNA-dependent	cytoplasm|nucleus	nucleotide binding|poly(A) RNA binding|protein binding|transcription coactivator activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(542;0.144)|Kidney(114;0.172)														---	---	---	---
TEX15	56154	broad.mit.edu	37	8	30723860	30723866	+	Intron	DEL	GAAAGGA	-	-	rs75189941	byFrequency;by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30723860_30723866delGAAAGGA	uc011lbc.1	-											Homo sapiens testis expressed 15, mRNA (cDNA clone IMAGE:8860305), partial cds.											ovary(3)|upper_aerodigestive_tract(2)|skin(2)	7				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	30824857	30824860	+	IGR	DEL	TGTG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30824857_30824860delTGTG								TEX15 (78635 upstream) : PURG (28461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	31098539	31098539	+	IGR	DEL	T	-	-	rs76662755		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31098539delT								WRN (67263 upstream) : NRG1 (398729 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	31147838	31147838	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31147838delT								WRN (116562 upstream) : NRG1 (349430 downstream)																																			---	---	---	---
NRG1	3084	broad.mit.edu	37	8	31649363	31649364	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31649363_31649364insT	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	31783511	31783512	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31783511_31783512insT	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	32079548	32079549	+	Intron	INS	-	AT	AT	rs150402572	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32079548_32079549insAT	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	32344937	32344937	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32344937delT	uc003xip.2	+							NM_013962	NP_039256			neuregulin 1 isoform GGF2						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	32794459	32794459	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32794459delT	uc003xjb.2	+											Homo sapiens cDNA clone IMAGE:4837650.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	32840079	32840080	+	Intron	DEL	AA	-	-	rs75540161		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32840079_32840080delAA	uc003xjb.2	+											Homo sapiens cDNA clone IMAGE:4837650.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	32865834	32865834	+	Intron	DEL	T	-	-	rs112718046		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32865834delT	uc003xjb.2	+											Homo sapiens cDNA clone IMAGE:4837650.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	32972450	32972450	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32972450delA								NRG1 (349892 upstream) : FUT10 (255896 downstream)																																			---	---	---	---
FUT10	84750	broad.mit.edu	37	8	33270537	33270538	+	Intron	INS	-	C	C	rs138746000	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33270537_33270538insC	uc003xje.2	-						FUT10_uc003xjc.2_Intron|FUT10_uc003xjd.2_Intron|FUT10_uc011lbi.1_Intron|FUT10_uc003xjf.2_Intron|FUT10_uc003xjg.2_Intron|FUT10_uc003xjh.2_Intron	NM_032664	NP_116053			fucosyltransferase 10						embryo development|fertilization|hemopoiesis|L-fucose catabolic process|nervous system development|protein folding|protein glycosylation|protein targeting|wound healing	Golgi cisterna membrane|integral to membrane	alpha(1,3)-fucosyltransferase activity			ovary(1)|pancreas(1)	2				KIRC - Kidney renal clear cell carcinoma(67;0.129)|Kidney(114;0.154)														---	---	---	---
FUT10	84750	broad.mit.edu	37	8	33305204	33305206	+	Intron	DEL	AGG	-	-	rs149681883		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33305204_33305206delAGG	uc003xje.2	-						FUT10_uc003xjc.2_Intron|FUT10_uc003xjd.2_Intron|FUT10_uc011lbi.1_Intron|FUT10_uc003xjf.2_Intron|FUT10_uc003xjg.2_Intron|FUT10_uc003xjh.2_Intron	NM_032664	NP_116053			fucosyltransferase 10						embryo development|fertilization|hemopoiesis|L-fucose catabolic process|nervous system development|protein folding|protein glycosylation|protein targeting|wound healing	Golgi cisterna membrane|integral to membrane	alpha(1,3)-fucosyltransferase activity			ovary(1)|pancreas(1)	2				KIRC - Kidney renal clear cell carcinoma(67;0.129)|Kidney(114;0.154)														---	---	---	---
C8orf41	80185	broad.mit.edu	37	8	33335627	33335628	+	Intron	INS	-	A	A	rs139394859	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33335627_33335628insA	uc010lvu.1	-											Homo sapiens cDNA: FLJ23263 fis, clone COL06129.								binding				0				KIRC - Kidney renal clear cell carcinoma(67;0.0923)|Kidney(114;0.111)														---	---	---	---
MAK16	84549	broad.mit.edu	37	8	33355017	33355019	+	Intron	DEL	AAT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33355017_33355019delAAT	uc003xjj.2	+						C8orf41_uc010lvu.1_Intron	NM_032509	NP_115898			MAK16 homolog							nucleolus				ovary(1)	1																		---	---	---	---
C8orf41	80185	broad.mit.edu	37	8	33367554	33367554	+	Intron	DEL	A	-	-	rs79956819		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33367554delA	uc003xjl.3	-						C8orf41_uc003xjk.3_Intron|C8orf41_uc010lvv.2_Intron|C8orf41_uc003xjm.3_Intron|C8orf41_uc003xjn.1_Intron	NM_025115	NP_079391			hypothetical protein LOC80185								binding				0				KIRC - Kidney renal clear cell carcinoma(67;0.0923)|Kidney(114;0.111)														---	---	---	---
DUSP26	78986	broad.mit.edu	37	8	33455401	33455402	+	Intron	DEL	AC	-	-	rs67461830		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33455401_33455402delAC	uc003xjp.2	-						DUSP26_uc003xjq.2_Intron	NM_024025	NP_076930			dual specificity phosphatase 26							Golgi apparatus|nucleus	protein binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0				KIRC - Kidney renal clear cell carcinoma(67;0.0918)|Kidney(114;0.111)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	33570501	33570501	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33570501delA								DUSP26 (113062 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	33798813	33798813	+	IGR	DEL	T	-	-	rs35824057		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33798813delT								DUSP26 (341374 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34944231	34944231	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34944231delT								None (None upstream) : UNC5D (148744 downstream)																																			---	---	---	---
UNC5D	137970	broad.mit.edu	37	8	35519985	35519985	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35519985delA	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)														---	---	---	---
KCNU1	157855	broad.mit.edu	37	8	36778228	36778229	+	Intron	INS	-	TG	TG			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36778228_36778229insTG	uc010lvw.2	+						KCNU1_uc003xjw.2_Intron	NM_001031836	NP_001027006			potassium channel, subfamily U, member 1							voltage-gated potassium channel complex	binding|large conductance calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	37171922	37171922	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37171922delT								KCNU1 (378281 upstream) : ZNF703 (381379 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37315370	37315372	+	IGR	DEL	TTA	-	-	rs7461155	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37315370_37315372delTTA								KCNU1 (521729 upstream) : ZNF703 (237929 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37381487	37381487	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37381487delA								KCNU1 (587846 upstream) : ZNF703 (171814 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37437284	37437284	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37437284delA								KCNU1 (643643 upstream) : ZNF703 (116017 downstream)																																			---	---	---	---
RAB11FIP1	80223	broad.mit.edu	37	8	37725231	37725231	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37725231delA	uc003xkm.1	-						RAB11FIP1_uc010lvz.1_Intron|RAB11FIP1_uc003xkn.1_Intron|RAB11FIP1_uc003xkl.1_Intron|RAB11FIP1_uc003xko.1_3'UTR|RAB11FIP1_uc003xkp.1_3'UTR	NM_001002814	NP_001002814			RAB11 family interacting protein 1 isoform 3						protein transport	centrosome|phagocytic vesicle membrane|recycling endosome	protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)															---	---	---	---
GOT1L1	137362	broad.mit.edu	37	8	37799532	37799534	+	5'Flank	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37799532_37799534delAAA	uc011lbj.1	-							NM_152413	NP_689626			glutamic-oxaloacetic transaminase 1-like 1						biosynthetic process|cellular amino acid metabolic process	cytoplasm	pyridoxal phosphate binding|transaminase activity			ovary(1)	1	Colorectal(12;0.00627)	Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;1.37e-11)															---	---	---	---
ASH2L	9070	broad.mit.edu	37	8	37964113	37964113	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37964113delC	uc003xkt.3	+						ASH2L_uc011lbk.1_Intron|ASH2L_uc003xku.3_Intron|ASH2L_uc010lwa.2_Intron	NM_004674	NP_004665			ash2-like isoform a						hemopoiesis|histone H3-K4 methylation|positive regulation of cell proliferation|regulation of transcription, DNA-dependent|response to estrogen stimulus|transcription from RNA polymerase II promoter	Set1C/COMPASS complex	metal ion binding|protein binding|transcription regulatory region DNA binding			ovary(1)|lung(1)	2	Colorectal(12;0.000501)	Lung NSC(58;0.0295)|all_lung(54;0.0413)																---	---	---	---
ASH2L	9070	broad.mit.edu	37	8	37988121	37988121	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37988121delT	uc003xkt.3	+						ASH2L_uc011lbk.1_Intron|ASH2L_uc003xku.3_Intron|ASH2L_uc010lwa.2_Intron	NM_004674	NP_004665			ash2-like isoform a						hemopoiesis|histone H3-K4 methylation|positive regulation of cell proliferation|regulation of transcription, DNA-dependent|response to estrogen stimulus|transcription from RNA polymerase II promoter	Set1C/COMPASS complex	metal ion binding|protein binding|transcription regulatory region DNA binding			ovary(1)|lung(1)	2	Colorectal(12;0.000501)	Lung NSC(58;0.0295)|all_lung(54;0.0413)																---	---	---	---
WHSC1L1	54904	broad.mit.edu	37	8	38168033	38168033	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38168033delT	uc003xli.2	-						WHSC1L1_uc011lbm.1_Intron|WHSC1L1_uc010lwe.2_Intron	NM_023034	NP_075447			WHSC1L1 protein isoform long						cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome	histone-lysine N-methyltransferase activity|zinc ion binding			breast(1)	1	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)					T	NUP98	AML								---	---	---	---
WHSC1L1	54904	broad.mit.edu	37	8	38241645	38241647	+	5'Flank	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38241645_38241647delTTT	uc003xli.2	-						WHSC1L1_uc011lbm.1_5'Flank|WHSC1L1_uc010lwe.2_5'Flank|WHSC1L1_uc003xlj.2_5'Flank|LETM2_uc003xlk.2_5'Flank|LETM2_uc011lbn.1_5'Flank|LETM2_uc003xll.1_5'Flank|LETM2_uc003xlm.1_5'Flank|LETM2_uc003xln.1_5'Flank	NM_023034	NP_075447			WHSC1L1 protein isoform long						cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome	histone-lysine N-methyltransferase activity|zinc ion binding			breast(1)	1	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)					T	NUP98	AML								---	---	---	---
TACC1	6867	broad.mit.edu	37	8	38661238	38661239	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38661238_38661239delTT	uc010lwp.2	+						TACC1_uc011lby.1_Intron|TACC1_uc003xma.2_Intron|TACC1_uc003xlz.2_Intron|TACC1_uc003xmc.3_Intron|TACC1_uc011lbz.1_Intron|TACC1_uc003xmb.3_Intron|TACC1_uc003xme.1_Intron|TACC1_uc003xmd.1_Intron|TACC1_uc010lwo.1_Intron|TACC1_uc003xmf.3_Intron|TACC1_uc011lca.1_Intron|TACC1_uc011lcb.1_Intron|TACC1_uc011lcc.1_5'Flank	NM_006283	NP_006274			transforming, acidic coiled-coil containing						cell cycle|cell division	intermediate filament cytoskeleton|microtubule organizing center|nucleus	protein binding			ovary(1)	1		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.065)	LUSC - Lung squamous cell carcinoma(45;1.7e-09)|COAD - Colon adenocarcinoma(9;0.235)															---	---	---	---
PLEKHA2	59339	broad.mit.edu	37	8	38783806	38783806	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38783806delA	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)															---	---	---	---
PLEKHA2	59339	broad.mit.edu	37	8	38816657	38816657	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38816657delT	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)															---	---	---	---
PLEKHA2	59339	broad.mit.edu	37	8	38825183	38825185	+	Intron	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38825183_38825185delTTT	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	38880562	38880562	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38880562delT	uc003xmr.2	+						ADAM9_uc011lcf.1_Intron|ADAM9_uc011lcg.1_Intron|ADAM9_uc010lwr.2_Intron	NM_003816	NP_003807			ADAM metallopeptidase domain 9 isoform 1						activation of MAPKK activity|cell-cell adhesion mediated by integrin|cell-matrix adhesion|keratinocyte differentiation|monocyte activation|PMA-inducible membrane protein ectodomain proteolysis|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell adhesion mediated by integrin|positive regulation of keratinocyte migration|positive regulation of macrophage fusion|positive regulation of membrane protein ectodomain proteolysis|positive regulation of protein secretion|response to calcium ion|response to glucocorticoid stimulus|response to hydrogen peroxide|response to manganese ion|response to tumor necrosis factor|transforming growth factor beta receptor signaling pathway	extracellular space|extracellular space|integral to membrane|intrinsic to external side of plasma membrane	collagen binding|integrin binding|laminin binding|metalloendopeptidase activity|protein kinase C binding|SH3 domain binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;2.74e-07)															---	---	---	---
ADAM9	8754	broad.mit.edu	37	8	38956852	38956852	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38956852delT	uc003xmr.2	+						ADAM9_uc011lcf.1_Intron|ADAM9_uc011lcg.1_Intron|ADAM9_uc010lwr.2_Intron|ADAM9_uc003xms.2_Intron	NM_003816	NP_003807			ADAM metallopeptidase domain 9 isoform 1						activation of MAPKK activity|cell-cell adhesion mediated by integrin|cell-matrix adhesion|keratinocyte differentiation|monocyte activation|PMA-inducible membrane protein ectodomain proteolysis|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell adhesion mediated by integrin|positive regulation of keratinocyte migration|positive regulation of macrophage fusion|positive regulation of membrane protein ectodomain proteolysis|positive regulation of protein secretion|response to calcium ion|response to glucocorticoid stimulus|response to hydrogen peroxide|response to manganese ion|response to tumor necrosis factor|transforming growth factor beta receptor signaling pathway	extracellular space|extracellular space|integral to membrane|intrinsic to external side of plasma membrane	collagen binding|integrin binding|laminin binding|metalloendopeptidase activity|protein kinase C binding|SH3 domain binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;2.74e-07)															---	---	---	---
ADAM32	203102	broad.mit.edu	37	8	39084055	39084055	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39084055delA	uc003xmt.3	+						ADAM32_uc011lch.1_Intron|ADAM32_uc003xmu.3_Intron|ADAM32_uc003xmv.2_Intron	NM_145004	NP_659441			a disintegrin and metalloprotease domain 32						proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)|kidney(1)	3		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	39977473	39977473	+	IGR	DEL	T	-	-	rs68075364		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39977473delT								IDO2 (103563 upstream) : C8orf4 (33516 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	39981347	39981348	+	IGR	INS	-	AG	AG	rs140039860	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39981347_39981348insAG								IDO2 (107437 upstream) : C8orf4 (29641 downstream)																																			---	---	---	---
ZMAT4	79698	broad.mit.edu	37	8	40641579	40641580	+	Intron	INS	-	ACC	ACC			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40641579_40641580insACC	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	40740229	40740230	+	Intron	INS	-	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40740229_40740230insC	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	40838684	40838684	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40838684delA								ZMAT4 (83341 upstream) : SFRP1 (280795 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	41762907	41762907	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41762907delA								ANK1 (8627 upstream) : MYST3 (24091 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	41778812	41778812	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41778812delA								ANK1 (24532 upstream) : MYST3 (8186 downstream)																																			---	---	---	---
MYST3	7994	broad.mit.edu	37	8	41801617	41801618	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41801617_41801618delAA	uc010lxb.2	-						MYST3_uc010lxc.2_Intron|MYST3_uc003xon.3_Intron|MYST3_uc010lxd.2_Intron	NM_001099412	NP_001092882			MYST histone acetyltransferase (monocytic						histone H3 acetylation|myeloid cell differentiation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription coactivator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1)	7	all_epithelial(6;1.12e-27)|all_lung(13;3.94e-12)|Lung NSC(13;6.54e-11)|Ovarian(28;0.00744)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000294)|Lung NSC(58;0.00105)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	Epithelial(1;2.82e-19)|all cancers(1;1.15e-16)|BRCA - Breast invasive adenocarcinoma(8;9.17e-11)|OV - Ovarian serous cystadenocarcinoma(14;9.4e-05)|Colorectal(10;0.000728)|Lung(22;0.00153)|LUSC - Lung squamous cell carcinoma(45;0.00741)|COAD - Colon adenocarcinoma(11;0.0171)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	41975205	41975205	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41975205delT								MYST3 (65700 upstream) : AP3M2 (35259 downstream)																																			---	---	---	---
AP3M2	10947	broad.mit.edu	37	8	42025824	42025824	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42025824delG	uc003xop.2	+						AP3M2_uc003xoo.2_Intron|AP3M2_uc010lxe.2_Intron	NM_001134296	NP_001127768			adaptor-related protein complex 3, mu 2 subunit						intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|Golgi apparatus					0	all_cancers(6;8.14e-25)|all_epithelial(6;2.41e-27)|all_lung(13;5.09e-13)|Lung NSC(13;8.38e-12)|Ovarian(28;0.00438)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	BRCA - Breast invasive adenocarcinoma(8;5.23e-10)|Colorectal(10;0.00165)|OV - Ovarian serous cystadenocarcinoma(14;0.00346)|Lung(22;0.00467)|COAD - Colon adenocarcinoma(11;0.0171)|LUSC - Lung squamous cell carcinoma(45;0.024)															---	---	---	---
PLAT	5327	broad.mit.edu	37	8	42064041	42064042	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42064041_42064042delAC	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	42117534	42117535	+	IGR	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42117534_42117535delAG								PLAT (52340 upstream) : IKBKB (11294 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	42453392	42453392	+	IGR	DEL	T	-	-	rs34116246		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42453392delT								C8orf40 (45253 upstream) : CHRNB3 (99170 downstream)																																			---	---	---	---
HOOK3	84376	broad.mit.edu	37	8	42765500	42765501	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42765500_42765501delTT	uc003xpr.2	+						HOOK3_uc010lxq.1_Intron	NM_032410	NP_115786			golgi-associated microtubule-binding protein						cytoplasmic microtubule organization|early endosome to late endosome transport|endosome organization|endosome to lysosome transport|Golgi localization|interkinetic nuclear migration|lysosome organization|microtubule anchoring|negative regulation of neurogenesis|protein localization to centrosome|protein transport	cis-Golgi network|FHF complex|microtubule|pericentriolar material	identical protein binding|microtubule binding			ovary(1)|breast(1)	2	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)					T	RET	papillary thyroid								---	---	---	---
Unknown	0	broad.mit.edu	37	8	42886349	42886349	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42886349delT								HOOK3 (668 upstream) : FNTA (25093 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	42899748	42899748	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42899748delT								HOOK3 (14067 upstream) : FNTA (11694 downstream)																																			---	---	---	---
FNTA	2339	broad.mit.edu	37	8	42918489	42918489	+	Intron	DEL	T	-	-	rs147258387		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42918489delT	uc003xps.2	+						FNTA_uc003xpt.2_Intron|FNTA_uc003xpu.2_Intron|FNTA_uc003xpv.2_Intron	NM_002027	NP_002018			farnesyltransferase, CAAX box, alpha isoform a						cellular component disassembly involved in apoptosis|positive regulation of deacetylase activity|positive regulation of tubulin deacetylation|protein farnesylation|protein geranylgeranylation|transforming growth factor beta receptor signaling pathway	cytosol|microtubule associated complex	alpha-tubulin binding|CAAX-protein geranylgeranyltransferase activity|microtubule binding|protein farnesyltransferase activity			ovary(1)	1	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	43330418	43330419	+	IGR	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43330418_43330419delCT								POTEA (112090 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	43350370	43350370	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43350370delT								POTEA (132042 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	43358982	43358982	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43358982delA								POTEA (140654 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	43403666	43403667	+	IGR	DEL	CC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43403666_43403667delCC								POTEA (185338 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	43528374	43528374	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43528374delG								POTEA (310046 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	43679978	43679978	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43679978delT								POTEA (461650 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	46907562	46907562	+	IGR	DEL	T	-	-	rs140128389		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:46907562delT								None (None upstream) : BEYLA (844946 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47151923	47151924	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47151923_47151924insA								None (None upstream) : BEYLA (600584 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47206540	47206540	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47206540delT								None (None upstream) : BEYLA (545968 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47250183	47250183	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47250183delA								None (None upstream) : BEYLA (502325 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47579857	47579858	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47579857_47579858delAA								None (None upstream) : BEYLA (172650 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47891384	47891384	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47891384delT								BEYLA (123977 upstream) : KIAA0146 (282158 downstream)																																			---	---	---	---
KIAA0146	23514	broad.mit.edu	37	8	48633045	48633045	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48633045delG	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)																---	---	---	---
MCM4	4173	broad.mit.edu	37	8	48874451	48874451	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48874451delT	uc003xqk.1	+						PRKDC_uc003xqi.2_5'Flank|PRKDC_uc003xqj.2_5'Flank|PRKDC_uc011ldh.1_5'Flank|MCM4_uc003xql.1_Intron|MCM4_uc011ldi.1_Intron|MCM4_uc010lxw.1_Intron	NM_182746	NP_877423			minichromosome maintenance complex component 4						cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	MCM complex	ATP binding|DNA binding|helicase activity|protein binding			ovary(2)|skin(2)	4		all_cancers(86;0.026)|all_epithelial(80;0.000748)|Lung NSC(129;0.00327)|all_lung(136;0.00354)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	49518726	49518726	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49518726delA								UBE2V2 (544274 upstream) : EFCAB1 (104625 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49533848	49533848	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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	49860786	49860787	+	IGR	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49860786_49860787delGT								SNAI2 (26798 upstream) : C8orf22 (124116 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	50120887	50120888	+	IGR	DEL	AG	-	-	rs34713424		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50120887_50120888delAG								C8orf22 (132246 upstream) : SNTG1 (701461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	50285017	50285017	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50285017delA								C8orf22 (296376 upstream) : SNTG1 (537332 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	50416997	50416999	+	IGR	DEL	TTT	-	-	rs11429448		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50416997_50416999delTTT								C8orf22 (428356 upstream) : SNTG1 (405350 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	50429701	50429701	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50429701delT								C8orf22 (441060 upstream) : SNTG1 (392648 downstream)																																			---	---	---	---
SNTG1	54212	broad.mit.edu	37	8	51172401	51172401	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51172401delT	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)																---	---	---	---
SNTG1	54212	broad.mit.edu	37	8	51461190	51461190	+	Intron	DEL	A	-	-	rs5891373		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51461190delA	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)																---	---	---	---
SNTG1	54212	broad.mit.edu	37	8	51651351	51651351	+	Intron	DEL	A	-	-	rs141177376		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51651351delA	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	51986133	51986134	+	IGR	INS	-	AAAC	AAAC			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51986133_51986134insAAAC								SNTG1 (280706 upstream) : PXDNL (246010 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	52075443	52075444	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52075443_52075444delTT								SNTG1 (370016 upstream) : PXDNL (156700 downstream)																																			---	---	---	---
PXDNL	137902	broad.mit.edu	37	8	52618391	52618398	+	Intron	DEL	GTGCGCGC	-	-	rs71828659	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52618391_52618398delGTGCGCGC	uc003xqu.3	-							NM_144651	NP_653252			peroxidasin homolog-like precursor						hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)																---	---	---	---
PXDNL	137902	broad.mit.edu	37	8	52627360	52627360	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52627360delG	uc003xqu.3	-							NM_144651	NP_653252			peroxidasin homolog-like precursor						hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)																---	---	---	---
PXDNL	137902	broad.mit.edu	37	8	52665812	52665812	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52665812delA	uc003xqu.3	-							NM_144651	NP_653252			peroxidasin homolog-like precursor						hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	52812672	52812672	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52812672delA	uc011ldp.1	+						PCMTD1_uc003xqx.3_5'Flank|PCMTD1_uc003xqw.3_5'Flank|PCMTD1_uc011ldn.1_5'Flank|PCMTD1_uc010lya.2_5'Flank					SubName: Full=cDNA FLJ58935;																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	52938591	52938592	+	IGR	DEL	AA	-	-	rs66566622		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52938591_52938592delAA								PCMTD1 (126856 upstream) : ST18 (84800 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	52951604	52951605	+	IGR	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52951604_52951605delCT								PCMTD1 (139869 upstream) : ST18 (71787 downstream)																																			---	---	---	---
ST18	9705	broad.mit.edu	37	8	53024509	53024510	+	3'UTR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53024509_53024510delTG	uc003xqz.2	-	21					ST18_uc011ldq.1_3'UTR|ST18_uc011ldr.1_3'UTR|ST18_uc011lds.1_3'UTR|ST18_uc003xra.2_3'UTR	NM_014682	NP_055497			suppression of tumorigenicity 18							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(1)	5		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	53399585	53399585	+	IGR	DEL	A	-	-	rs10709849		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53399585delA								ST18 (77146 upstream) : FAM150A (47013 downstream)																																			---	---	---	---
RB1CC1	9821	broad.mit.edu	37	8	53579079	53579080	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53579079_53579080delAA	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	53849224	53849224	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53849224delA								RB1CC1 (222198 upstream) : NPBWR1 (3244 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	53952794	53952794	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53952794delT								NPBWR1 (99341 upstream) : OPRK1 (185482 downstream)																																			---	---	---	---
OPRK1	4986	broad.mit.edu	37	8	54148694	54148694	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54148694delC	uc003xrh.1	-						OPRK1_uc003xri.1_Intron|OPRK1_uc010lyc.1_Intron	NM_000912	NP_000903			opioid receptor, kappa 1						behavior|immune response|inhibition of adenylate cyclase activity by G-protein signaling pathway|sensory perception|synaptic transmission|viral genome replication	integral to plasma membrane	kappa-opioid receptor activity|protein binding			ovary(1)|skin(1)	2		all_epithelial(80;0.066)|Lung NSC(129;0.0804)|all_lung(136;0.136)			Buprenorphine(DB00921)|Butorphanol(DB00611)|Cocaine(DB00907)|Codeine(DB00318)|Dezocine(DB01209)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Meperidine(DB00454)|Mirtazapine(DB00370)|Morphine(DB00295)|Nalbuphine(DB00844)|Naltrexone(DB00704)|Oxycodone(DB00497)|Pentazocine(DB00652)|Propoxyphene(DB00647)|Tramadol(DB00193)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	54467293	54467293	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54467293delA								OPRK1 (303099 upstream) : ATP6V1H (160823 downstream)																																			---	---	---	---
ATP6V1H	51606	broad.mit.edu	37	8	54657265	54657265	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54657265delA	uc003xrl.2	-						ATP6V1H_uc003xrk.2_Intron|ATP6V1H_uc003xrm.2_Intron|ATP6V1H_uc003xrn.2_Intron|ATP6V1H_uc011ldv.1_Intron|ATP6V1H_uc010lyd.2_Intron	NM_213620	NP_998785			ATPase, H+ transporting, lysosomal 50/57kDa, V1						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|endocytosis|insulin receptor signaling pathway|interspecies interaction between organisms|regulation of defense response to virus by virus|transferrin transport|vacuolar acidification|viral reproduction	cytosol|plasma membrane|vacuolar proton-transporting V-type ATPase, V1 domain	enzyme regulator activity|protein binding|proton-transporting ATPase activity, rotational mechanism				0		all_epithelial(80;0.0487)|Lung NSC(129;0.109)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;2.79e-06)|Epithelial(17;0.000629)|all cancers(17;0.00359)															---	---	---	---
RGS20	8601	broad.mit.edu	37	8	54765495	54765495	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54765495delA	uc003xrp.2	+						RGS20_uc003xrq.2_Intron|RGS20_uc010lye.2_Intron|RGS20_uc010lyf.2_Intron	NM_170587	NP_733466			regulator of G-protein signaling 20 isoform a						negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|nucleus|plasma membrane	GTPase activator activity|protein binding|signal transducer activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(7;1.37e-06)|Epithelial(17;0.000126)|all cancers(17;0.0009)															---	---	---	---
RGS20	8601	broad.mit.edu	37	8	54773528	54773528	+	Intron	DEL	A	-	-	rs78507684		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54773528delA	uc003xrp.2	+						RGS20_uc003xrq.2_Intron|RGS20_uc010lye.2_Intron|RGS20_uc010lyf.2_Intron	NM_170587	NP_733466			regulator of G-protein signaling 20 isoform a						negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|nucleus|plasma membrane	GTPase activator activity|protein binding|signal transducer activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(7;1.37e-06)|Epithelial(17;0.000126)|all cancers(17;0.0009)															---	---	---	---
TCEA1	6917	broad.mit.edu	37	8	54899493	54899493	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54899493delA	uc003xru.2	-						TCEA1_uc003xrv.2_Intron|TCEA1_uc011ldw.1_Intron|TCEA1_uc010lyg.2_5'Flank	NM_006756	NP_006747			transcription elongation factor A 1 isoform 1						positive regulation of viral transcription|regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription elongation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	nucleoplasm	DNA binding|translation elongation factor activity|zinc ion binding				0		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;9.1e-07)|Epithelial(17;9.44e-05)|all cancers(17;0.000699)					T	PLAG1	salivary adenoma								---	---	---	---
LYPLA1	10434	broad.mit.edu	37	8	55010783	55010783	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55010783delA	uc003xry.2	-						LYPLA1_uc011ldx.1_Intron|LYPLA1_uc003xrz.2_Intron	NM_006330	NP_006321			lysophospholipase 1						fatty acid metabolic process|nitric oxide metabolic process|regulation of nitric-oxide synthase activity	cytosol	lysophospholipase activity|palmitoyl-(protein) hydrolase activity			central_nervous_system(1)	1		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;8.48e-07)|Epithelial(17;9.29e-05)|all cancers(17;0.000689)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	55822610	55822610	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55822610delT								RP1 (140079 upstream) : XKR4 (192407 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55884651	55884651	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55884651delT								RP1 (202120 upstream) : XKR4 (130366 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	56512615	56512615	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56512615delT								XKR4 (73907 upstream) : TMEM68 (138705 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	56576306	56576308	+	IGR	DEL	TTG	-	-	rs71555611		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56576306_56576308delTTG								XKR4 (137598 upstream) : TMEM68 (75012 downstream)																																			---	---	---	---
TGS1	96764	broad.mit.edu	37	8	56708828	56708828	+	Intron	DEL	T	-	-	rs111385978		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56708828delT	uc003xsj.3	+						TGS1_uc010lyh.2_Intron	NM_024831	NP_079107			trimethylguanosine synthase homolog						cellular lipid metabolic process|ncRNA metabolic process|regulation of transcription, DNA-dependent|RNA capping|spliceosomal snRNP assembly|transcription, DNA-dependent	Cajal body|cytosol	RNA trimethylguanosine synthase activity			ovary(1)|lung(1)|breast(1)	3		all_lung(136;0.119)|all_epithelial(80;0.125)|Lung NSC(129;0.147)	Epithelial(17;0.00027)|all cancers(17;0.00251)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	56939986	56939986	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56939986delA								LYN (16050 upstream) : RPS20 (40753 downstream)																																			---	---	---	---
CHCHD7	79145	broad.mit.edu	37	8	57129755	57129756	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57129755_57129756insT	uc003xsx.2	+						CHCHD7_uc003xss.2_Intron|CHCHD7_uc003xst.2_Intron|CHCHD7_uc003xsu.2_Intron|CHCHD7_uc003xsv.2_Intron|CHCHD7_uc003xsw.2_Intron	NM_001011671	NP_001011671			coiled-coil-helix-coiled-coil-helix domain										CHCHD7/PLAG1(12)	salivary_gland(12)	12		all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.125)	Epithelial(17;0.00159)|all cancers(17;0.0112)					T	PLAG1	salivary adenoma								---	---	---	---
Unknown	0	broad.mit.edu	37	8	57389315	57389320	+	Intron	DEL	TTTTGT	-	-	rs139803575	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57389315_57389320delTTTTGT	uc003xtb.1	+											Homo sapiens cDNA FLJ34244 fis, clone FCBBF3028794.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	57394552	57394552	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57394552delT	uc003xtb.1	+											Homo sapiens cDNA FLJ34244 fis, clone FCBBF3028794.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	57541376	57541378	+	IGR	DEL	ACA	-	-	rs72418748		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57541376_57541378delACA								PENK (182094 upstream) : IMPAD1 (329113 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	57589213	57589216	+	IGR	DEL	CTTG	-	-	rs148530613		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57589213_57589216delCTTG								PENK (229931 upstream) : IMPAD1 (281275 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	57994838	57994839	+	IGR	INS	-	AAAC	AAAC	rs146408174	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57994838_57994839insAAAC								IMPAD1 (88411 upstream) : C8orf71 (197263 downstream)																																			---	---	---	---
FAM110B	90362	broad.mit.edu	37	8	59050119	59050120	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59050119_59050120delAA	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	59230840	59230840	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59230840delA								FAM110B (168563 upstream) : UBXN2B (92983 downstream)																																	OREG0018785	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CYP7A1	1581	broad.mit.edu	37	8	59404655	59404655	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59404655delA	uc003xtm.3	-							NM_000780	NP_000771			cytochrome P450, family 7, subfamily A,						bile acid biosynthetic process|cellular lipid metabolic process|cellular response to cholesterol|cellular response to glucose stimulus|cholesterol catabolic process|cholesterol homeostasis|regulation of bile acid biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	cholesterol 7-alpha-monooxygenase activity|electron carrier activity|heme binding			ovary(1)	1		all_lung(136;0.0271)|Lung NSC(129;0.0351)|all_epithelial(80;0.0554)												Neonatal_Giant_Cell_Hepatitis				---	---	---	---
TOX	9760	broad.mit.edu	37	8	59740583	59740583	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59740583delA	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	59769308	59769308	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59769308delT	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	59911966	59911966	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59911966delA	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	59937316	59937316	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59937316delA	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	60201133	60201134	+	IGR	INS	-	TG	TG			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60201133_60201134insTG								TOX (169366 upstream) : CA8 (900289 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	60708523	60708523	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60708523delA								TOX (676756 upstream) : CA8 (392900 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	61424442	61424442	+	IGR	DEL	T	-	-	rs34046281		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61424442delT								CA8 (230488 upstream) : RAB2A (5117 downstream)																																			---	---	---	---
CHD7	55636	broad.mit.edu	37	8	61714076	61714076	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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	61720893	61720893	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61720893delT	uc003xue.2	+							NM_017780	NP_060250			chromodomain helicase DNA binding protein 7						central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity	p.556_871dup(1)		ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	61981534	61981534	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61981534delT								CHD7 (202071 upstream) : CLVS1 (218991 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	62164518	62164518	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62164518delT								CHD7 (385055 upstream) : CLVS1 (36007 downstream)																																			---	---	---	---
CLVS1	157807	broad.mit.edu	37	8	62278336	62278337	+	Intron	DEL	GT	-	-	rs112942345		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62278336_62278337delGT	uc003xuh.2	+						CLVS1_uc003xug.2_Intron|CLVS1_uc003xui.2_Intron|CLVS1_uc010lyp.2_Intron	NM_173519	NP_775790			retinaldehyde binding protein 1-like 1						lysosome organization	clathrin-coated vesicle|early endosome membrane|trans-Golgi network	phosphatidylinositol-3,5-bisphosphate binding|transporter activity			skin(4)|ovary(1)	5																		---	---	---	---
CLVS1	157807	broad.mit.edu	37	8	62362211	62362211	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62362211delT	uc003xuh.2	+						CLVS1_uc003xui.2_Intron|CLVS1_uc010lyp.2_Intron	NM_173519	NP_775790			retinaldehyde binding protein 1-like 1						lysosome organization	clathrin-coated vesicle|early endosome membrane|trans-Golgi network	phosphatidylinositol-3,5-bisphosphate binding|transporter activity			skin(4)|ovary(1)	5																		---	---	---	---
ASPH	444	broad.mit.edu	37	8	62565088	62565088	+	Intron	DEL	A	-	-	rs34800191		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62565088delA	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	62726023	62726023	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62726023delA								ASPH (98824 upstream) : NKAIN3 (435478 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	62829182	62829182	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62829182delA								ASPH (201983 upstream) : NKAIN3 (332319 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	62887806	62887806	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62887806delT								ASPH (260607 upstream) : NKAIN3 (273695 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	62963303	62963303	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62963303delA								ASPH (336104 upstream) : NKAIN3 (198198 downstream)																																			---	---	---	---
NKAIN3	286183	broad.mit.edu	37	8	63301442	63301443	+	Intron	DEL	TG	-	-	rs10554062		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63301442_63301443delTG	uc010lyq.1	+							NM_173688	NP_775959			Na+/K+ transporting ATPase interacting 3							integral to membrane|plasma membrane					0	Breast(64;0.127)	Lung NSC(129;0.187)																---	---	---	---
NKAIN3	286183	broad.mit.edu	37	8	63631297	63631297	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63631297delT	uc010lyq.1	+							NM_173688	NP_775959			Na+/K+ transporting ATPase interacting 3							integral to membrane|plasma membrane					0	Breast(64;0.127)	Lung NSC(129;0.187)																---	---	---	---
NKAIN3	286183	broad.mit.edu	37	8	63653922	63653929	+	Intron	DEL	GAAGGAAG	-	-	rs72466142	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63653922_63653929delGAAGGAAG	uc010lyq.1	+							NM_173688	NP_775959			Na+/K+ transporting ATPase interacting 3							integral to membrane|plasma membrane					0	Breast(64;0.127)	Lung NSC(129;0.187)																---	---	---	---
YTHDF3	253943	broad.mit.edu	37	8	64124995	64124995	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64124995delA	uc003xuy.2	+	6					YTHDF3_uc010lys.2_3'UTR|YTHDF3_uc003xuz.2_3'UTR|YTHDF3_uc003xva.2_3'UTR|YTHDF3_uc011len.1_3'UTR	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	64390517	64390518	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64390517_64390518insA								YTHDF3 (265172 upstream) : MIR124-2 (901188 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	64454672	64454672	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64454672delT								YTHDF3 (329327 upstream) : MIR124-2 (837034 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	64515496	64515496	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64515496delG								YTHDF3 (390151 upstream) : MIR124-2 (776210 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	64588044	64588044	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64588044delT								YTHDF3 (462699 upstream) : MIR124-2 (703662 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	64721029	64721029	+	IGR	DEL	T	-	-	rs78720461		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64721029delT								YTHDF3 (595684 upstream) : MIR124-2 (570677 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	65279168	65279169	+	IGR	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65279168_65279169delAG								None (None upstream) : MIR124-2 (12537 downstream)																																			---	---	---	---
CYP7B1	9420	broad.mit.edu	37	8	65638734	65638734	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65638734delA	uc003xvj.2	-							NM_004820	NP_004811			cytochrome P450, family 7, subfamily B,						bile acid biosynthetic process|cell death|cholesterol metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	25-hydroxycholesterol 7alpha-hydroxylase activity|electron carrier activity|heme binding|oxysterol 7-alpha-hydroxylase activity			ovary(3)	3		all_cancers(86;0.217)|Lung NSC(129;0.0521)|all_lung(136;0.0906)|all_epithelial(80;0.215)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	65833147	65833147	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65833147delT								CYP7B1 (121799 upstream) : ARMC1 (681925 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	65974700	65974700	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65974700delA								CYP7B1 (263352 upstream) : ARMC1 (540372 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	66123874	66123875	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66123874_66123875delAA								CYP7B1 (412526 upstream) : ARMC1 (391197 downstream)																																			---	---	---	---
MTFR1	9650	broad.mit.edu	37	8	66570859	66570860	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66570859_66570860delAC	uc003xvm.2	+						MTFR1_uc011lep.1_Intron	NM_014637	NP_055452			mitochondrial fission regulator 1 isoform 1							mitochondrion|plasma membrane				pancreas(1)	1			Epithelial(68;0.0526)|BRCA - Breast invasive adenocarcinoma(89;0.156)|all cancers(69;0.171)|OV - Ovarian serous cystadenocarcinoma(28;0.194)															---	---	---	---
PDE7A	5150	broad.mit.edu	37	8	66648919	66648919	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66648919delA	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)													---	---	---	---
PDE7A	5150	broad.mit.edu	37	8	66663040	66663040	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66663040delA	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)													---	---	---	---
PDE7A	5150	broad.mit.edu	37	8	66685511	66685512	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66685511_66685512insA	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	67177075	67177081	+	IGR	DEL	AAAAAAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67177075_67177081delAAAAAAA								CRH (86377 upstream) : RRS1 (164182 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	67309272	67309272	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67309272delA								CRH (218574 upstream) : RRS1 (31991 downstream)																																			---	---	---	---
SGK3	23678	broad.mit.edu	37	8	67681467	67681467	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67681467delT	uc003xwr.2	+						SGK3_uc003xwp.2_Intron|PTTG3P_uc011leu.1_5'Flank	NM_001033578	NP_001028750			serum/glucocorticoid regulated kinase 3 isoform						cell communication|response to stress	cytoplasmic membrane-bounded vesicle|early endosome	ATP binding|phosphatidylinositol binding|protein serine/threonine kinase activity			ovary(1)|large_intestine(1)|lung(1)|breast(1)	4	Breast(64;0.186)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0046)|OV - Ovarian serous cystadenocarcinoma(28;0.0112)|all cancers(69;0.0141)|BRCA - Breast invasive adenocarcinoma(89;0.206)															---	---	---	---
C8orf45	157777	broad.mit.edu	37	8	67791177	67791177	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67791177delA	uc003xwz.3	+						C8orf45_uc003xwv.2_Intron|C8orf45_uc011lev.1_Intron|C8orf45_uc011lew.1_Intron|C8orf45_uc011lex.1_Intron|C8orf45_uc003xwy.3_Intron	NM_173518	NP_775789			minichromosome maintenance complex						DNA replication		ATP binding|DNA binding			ovary(1)	1	Breast(64;0.186)		Epithelial(68;0.00384)|OV - Ovarian serous cystadenocarcinoma(28;0.00913)|all cancers(69;0.0175)|BRCA - Breast invasive adenocarcinoma(89;0.206)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	67867617	67867619	+	IGR	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67867617_67867619delAAA								SNHG6 (29840 upstream) : LRRC67 (32749 downstream)																																			---	---	---	---
CSPP1	79848	broad.mit.edu	37	8	68044403	68044403	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68044403delA	uc003xxi.2	+						CSPP1_uc003xxg.1_Intron|CSPP1_uc003xxh.1_Intron|CSPP1_uc003xxj.2_Intron|CSPP1_uc003xxk.2_Intron	NM_001077204	NP_001070672			centrosome spindle pole associated protein 1							centrosome|microtubule|spindle				ovary(3)|breast(2)	5	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	68319333	68319333	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68319333delA								ARFGEF1 (63421 upstream) : CPA6 (15073 downstream)																																			---	---	---	---
CPA6	57094	broad.mit.edu	37	8	68611825	68611826	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68611825_68611826delTT	uc003xxq.3	-						CPA6_uc003xxr.3_Intron|CPA6_uc003xxs.2_Intron	NM_020361	NP_065094			carboxypeptidase A6 isoform 1 precursor						proteolysis	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)															---	---	---	---
PREX2	80243	broad.mit.edu	37	8	68909478	68909478	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68909478delT	uc003xxv.1	+						PREX2_uc003xxu.1_Intron|PREX2_uc011lez.1_Intron	NM_024870	NP_079146			DEP domain containing 2 isoform a						G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17																		---	---	---	---
C8orf34	116328	broad.mit.edu	37	8	69427500	69427500	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69427500delT	uc010lyz.2	+						C8orf34_uc010lyy.1_Intron|C8orf34_uc003xyb.2_Intron	NM_052958	NP_443190			hypothetical protein LOC116328						signal transduction		cAMP-dependent protein kinase regulator activity			large_intestine(1)	1			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)															---	---	---	---
C8orf34	116328	broad.mit.edu	37	8	69699867	69699867	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69699867delA	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	69816079	69816079	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69816079delA								C8orf34 (84823 upstream) : SULF1 (562780 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	70279775	70279775	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70279775delT								C8orf34 (548519 upstream) : SULF1 (99084 downstream)																																			---	---	---	---
SLCO5A1	81796	broad.mit.edu	37	8	70603899	70603899	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70603899delT	uc003xyl.2	-						SLCO5A1_uc010lzb.2_Intron|SLCO5A1_uc011lfa.1_Intron|SLCO5A1_uc003xyk.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	70785022	70785022	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70785022delA								SLCO5A1 (37723 upstream) : PRDM14 (179003 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	70850245	70850245	+	IGR	DEL	A	-	-	rs5892219		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70850245delA								SLCO5A1 (102946 upstream) : PRDM14 (113780 downstream)																																			---	---	---	---
NCOA2	10499	broad.mit.edu	37	8	71313785	71313785	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71313785delT	uc003xyn.1	-							NM_006540	NP_006531			nuclear receptor coactivator 2						cellular lipid metabolic process|transcription, DNA-dependent	nucleoplasm	histone acetyltransferase activity|ligand-dependent nuclear receptor binding|nuclear hormone receptor binding|signal transducer activity		PAX3/NCOA2(4)	lung(6)|soft_tissue(4)|breast(2)|skin(2)|ovary(1)|pancreas(1)	16	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)					T	RUNXBP2	AML								---	---	---	---
Unknown	0	broad.mit.edu	37	8	71441537	71441537	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71441537delA								NCOA2 (125517 upstream) : TRAM1 (44136 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	71457886	71457887	+	IGR	INS	-	TG	TG	rs10665617		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71457886_71457887insTG								NCOA2 (141866 upstream) : TRAM1 (27786 downstream)																																			---	---	---	---
EYA1	2138	broad.mit.edu	37	8	72206261	72206261	+	Intron	DEL	A	-	-	rs4738124	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72206261delA	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	72406581	72406582	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72406581_72406582insT	uc003xyw.2	-											Homo sapiens cDNA clone IMAGE:5264099.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	72639097	72639098	+	IGR	DEL	TG	-	-	rs112615173		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72639097_72639098delTG								EYA1 (364630 upstream) : MSC (114679 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	72705088	72705088	+	IGR	DEL	T	-	-	rs57294932		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72705088delT								EYA1 (430621 upstream) : MSC (48689 downstream)																																			---	---	---	---
KCNB2	9312	broad.mit.edu	37	8	73465108	73465108	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73465108delT	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	73530420	73530420	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73530420delA	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	73901121	73901121	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73901121delA								KCNB2 (50539 upstream) : TERF1 (19976 downstream)																																			---	---	---	---
STAU2	27067	broad.mit.edu	37	8	74343584	74343584	+	Intron	DEL	G	-	-	rs56291509		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74343584delG	uc003xzm.2	-						STAU2_uc011lfg.1_Intron|STAU2_uc003xzn.2_Intron|STAU2_uc011lfh.1_Intron|uc003xzl.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)															---	---	---	---
STAU2	27067	broad.mit.edu	37	8	74598784	74598787	+	Intron	DEL	AAAA	-	-	rs111707785		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74598784_74598787delAAAA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	74993500	74993500	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74993500delT								LY96 (52195 upstream) : JPH1 (153441 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	75117607	75117607	+	IGR	DEL	T	-	-	rs76380464		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75117607delT								LY96 (176302 upstream) : JPH1 (29334 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	75392222	75392228	+	IGR	DEL	TTTTTTT	-	-	rs149543770		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75392222_75392228delTTTTTTT								GDAP1 (112889 upstream) : MIR2052 (225700 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	75439973	75439973	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75439973delT								GDAP1 (160640 upstream) : MIR2052 (177955 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	75695549	75695549	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75695549delA								MIR2052 (77567 upstream) : PI15 (41223 downstream)																																			---	---	---	---
PI15	51050	broad.mit.edu	37	8	75748793	75748793	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75748793delA	uc003yal.2	+						uc003yak.1_Intron|PI15_uc003yam.2_Intron	NM_015886	NP_056970			protease inhibitor 15 preproprotein							extracellular region	peptidase inhibitor activity			central_nervous_system(2)|ovary(1)	3	Breast(64;0.137)		BRCA - Breast invasive adenocarcinoma(89;0.104)|Epithelial(68;0.118)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	76245743	76245743	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76245743delT								CRISPLD1 (298952 upstream) : HNF4G (74440 downstream)																																			---	---	---	---
HNF4G	3174	broad.mit.edu	37	8	76386096	76386096	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76386096delA	uc003yaq.2	+						HNF4G_uc003yap.1_Intron	NM_004133	NP_004124			hepatocyte nuclear factor 4, gamma						endocrine pancreas development|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)	1	Breast(64;0.0448)		BRCA - Breast invasive adenocarcinoma(89;0.161)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	77083748	77083748	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77083748delA								HNF4G (604689 upstream) : LOC100192378 (439367 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	77156846	77156846	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77156846delT								HNF4G (677787 upstream) : LOC100192378 (366269 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	77512322	77512323	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77512322_77512323insT								None (None upstream) : LOC100192378 (10792 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	77947522	77947523	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77947522_77947523delTC								PEX2 (34998 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78149419	78149419	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78149419delT								PEX2 (236895 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78405541	78405541	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78405541delA								PEX2 (493017 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78949488	78949488	+	IGR	DEL	A	-	-	rs76383470		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78949488delA								None (None upstream) : PKIA (478848 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	79144830	79144831	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79144830_79144831delTT								None (None upstream) : PKIA (283505 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	79294509	79294509	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79294509delT								None (None upstream) : PKIA (133827 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	79402267	79402267	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79402267delA								None (None upstream) : PKIA (26069 downstream)																																			---	---	---	---
FAM164A	51101	broad.mit.edu	37	8	79617040	79617040	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79617040delT	uc003ybd.2	+							NM_016010	NP_057094			hypothetical protein LOC51101											ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	80025540	80025540	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80025540delA								IL7 (307782 upstream) : STMN2 (497840 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	80317013	80317014	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80317013_80317014delTC								IL7 (599255 upstream) : STMN2 (206366 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	80391828	80391828	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80391828delT								IL7 (674070 upstream) : STMN2 (131552 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	80666606	80666606	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80666606delT								STMN2 (88212 upstream) : HEY1 (9640 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	81136187	81136187	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81136187delA								TPD52 (52351 upstream) : ZBTB10 (261667 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	81173475	81173475	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81173475delT								TPD52 (89639 upstream) : ZBTB10 (224379 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	81275871	81275871	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81275871delA								TPD52 (192035 upstream) : ZBTB10 (121983 downstream)																																			---	---	---	---
ZBTB10	65986	broad.mit.edu	37	8	81404720	81404720	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81404720delT	uc003ybx.3	+						ZBTB10_uc003ybv.3_Intron|ZBTB10_uc003ybw.3_Intron|ZBTB10_uc010lzt.2_Intron	NM_001105539	NP_001099009			zinc finger and BTB domain containing 10 isoform						transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			lung(1)	1	all_cancers(3;1.68e-09)|all_epithelial(4;5.13e-11)|Lung NSC(7;1.75e-07)|all_lung(9;7.38e-07)|Breast(3;2.96e-06)		BRCA - Breast invasive adenocarcinoma(6;0.000434)|Epithelial(68;0.00486)|all cancers(69;0.0296)															---	---	---	---
ZBTB10	65986	broad.mit.edu	37	8	81407650	81407650	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81407650delT	uc003ybx.3	+						ZBTB10_uc003ybv.3_Intron|ZBTB10_uc003ybw.3_Intron|ZBTB10_uc010lzt.2_Intron	NM_001105539	NP_001099009			zinc finger and BTB domain containing 10 isoform						transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			lung(1)	1	all_cancers(3;1.68e-09)|all_epithelial(4;5.13e-11)|Lung NSC(7;1.75e-07)|all_lung(9;7.38e-07)|Breast(3;2.96e-06)		BRCA - Breast invasive adenocarcinoma(6;0.000434)|Epithelial(68;0.00486)|all cancers(69;0.0296)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	81460709	81460709	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81460709delT								ZBTB10 (26101 upstream) : ZNF704 (90060 downstream)																																			---	---	---	---
ZNF704	619279	broad.mit.edu	37	8	81690484	81690484	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81690484delA	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	81832012	81832012	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81832012delT								ZNF704 (44996 upstream) : PAG1 (48036 downstream)																																			---	---	---	---
ZFAND1	79752	broad.mit.edu	37	8	82625928	82625928	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82625928delA	uc003ycj.1	-						ZFAND1_uc010lzx.1_Intron|ZFAND1_uc003yck.1_Intron	NM_024699	NP_078975			zinc finger, AN1-type domain 1								zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	83684828	83684828	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:83684828delA								SNX16 (930307 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84005562	84005562	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84005562delC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84579619	84579619	+	IGR	DEL	T	-	-	rs71522912		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84579619delT								None (None upstream) : RALYL (515834 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84890563	84890564	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84890563_84890564delAC								None (None upstream) : RALYL (204889 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84890990	84890990	+	IGR	DEL	A	-	-	rs34687139		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84890990delA								None (None upstream) : RALYL (204463 downstream)																																			---	---	---	---
RALYL	138046	broad.mit.edu	37	8	85219721	85219721	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85219721delA	uc003ycq.3	+						RALYL_uc003ycr.3_Intron|RALYL_uc003ycs.3_Intron|RALYL_uc010lzy.2_Intron|RALYL_uc003yct.3_Intron	NM_001100392	NP_001093862			RALY RNA binding protein-like isoform 2								identical protein binding|nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
RALYL	138046	broad.mit.edu	37	8	85567757	85567757	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85567757delT	uc003ycq.3	+						RALYL_uc003ycr.3_Intron|RALYL_uc003ycs.3_Intron|RALYL_uc010lzy.2_Intron|RALYL_uc003yct.3_Intron	NM_001100392	NP_001093862			RALY RNA binding protein-like isoform 2								identical protein binding|nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
RALYL	138046	broad.mit.edu	37	8	85574178	85574180	+	Intron	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85574178_85574180delTTT	uc003ycq.3	+						RALYL_uc003ycr.3_Intron|RALYL_uc003ycs.3_Intron|RALYL_uc010lzy.2_Intron|RALYL_uc003yct.3_Intron	NM_001100392	NP_001093862			RALY RNA binding protein-like isoform 2								identical protein binding|nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
C8orf59	401466	broad.mit.edu	37	8	86127123	86127123	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86127123delA	uc010mac.1	-						C8orf59_uc003ydd.2_Intron|C8orf59_uc010mad.1_Intron|C8orf59_uc003yde.2_Intron|uc003ydc.1_RNA|C8orf59_uc011lfu.1_Intron	NM_001099670	NP_001093140			hypothetical protein LOC401466												0																		---	---	---	---
CA13	377677	broad.mit.edu	37	8	86196369	86196369	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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																		---	---	---	---
CA13	377677	broad.mit.edu	37	8	86327422	86327422	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86327422delA	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	87100614	87100615	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87100614_87100615delTT								PSKH2 (18763 upstream) : ATP6V0D2 (10524 downstream)																																			---	---	---	---
ATP6V0D2	245972	broad.mit.edu	37	8	87132627	87132628	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87132627_87132628insA	uc003ydp.1	+							NM_152565	NP_689778			ATPase, H+ transporting, lysosomal 38kDa, V0						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	apical plasma membrane|endosome membrane|proton-transporting V-type ATPase, V0 domain|vacuolar proton-transporting V-type ATPase complex	hydrogen ion transmembrane transporter activity|protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	87323154	87323154	+	IGR	DEL	A	-	-	rs11343975		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87323154delA								SLC7A13 (80545 upstream) : WWP1 (31840 downstream)																																			---	---	---	---
CNGB3	54714	broad.mit.edu	37	8	87622048	87622048	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87622048delA	uc003ydx.2	-						CNGB3_uc010maj.2_Intron	NM_019098	NP_061971			cyclic nucleotide gated channel beta 3						signal transduction|visual perception	integral to membrane	cGMP binding			ovary(2)|pancreas(1)	3																		---	---	---	---
CNGB3	54714	broad.mit.edu	37	8	87651179	87651180	+	Intron	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87651179_87651180delTC	uc003ydx.2	-						CNGB3_uc010maj.2_Intron	NM_019098	NP_061971			cyclic nucleotide gated channel beta 3						signal transduction|visual perception	integral to membrane	cGMP binding			ovary(2)|pancreas(1)	3																		---	---	---	---
CNBD1	168975	broad.mit.edu	37	8	87944927	87944927	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87944927delA	uc003ydy.2	+							NM_173538	NP_775809			cyclic nucleotide binding domain containing 1											ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	88727446	88727447	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88727446_88727447delTG								CNBD1 (332491 upstream) : DCAF4L2 (155526 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	89004224	89004224	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89004224delT								DCAF4L2 (117928 upstream) : MMP16 (45238 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	89492227	89492227	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89492227delA								MMP16 (152510 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	90392466	90392466	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90392466delT								None (None upstream) : RIPK2 (377509 downstream)																																			---	---	---	---
RIPK2	8767	broad.mit.edu	37	8	90798702	90798702	+	Intron	DEL	A	-	-	rs112047259		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90798702delA	uc003yee.2	+						RIPK2_uc003yef.2_Intron	NM_003821	NP_003812			receptor-interacting serine-threonine kinase 2						activation of MAPK activity|anti-apoptosis|apoptosis|inflammatory response|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of protein ubiquitination|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|CARD domain binding|LIM domain binding|protein homodimerization activity|protein serine/threonine kinase activity|signal transducer activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(11;0.0474)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	91263365	91263365	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91263365delT								CALB1 (155678 upstream) : TMEM64 (370858 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	91373161	91373162	+	IGR	INS	-	A	A	rs142325347	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91373161_91373162insA								CALB1 (265474 upstream) : TMEM64 (261061 downstream)																																			---	---	---	---
TMEM64	169200	broad.mit.edu	37	8	91637754	91637755	+	3'UTR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91637754_91637755delAA	uc003yen.2	-	3					TMEM64_uc003yeo.2_3'UTR|TMEM64_uc011lgf.1_3'UTR	NM_001008495	NP_001008495			transmembrane protein 64 isoform 1							integral to membrane					0			BRCA - Breast invasive adenocarcinoma(11;0.0598)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	91988160	91988161	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91988160_91988161delAA								NECAB1 (16531 upstream) : TMEM55A (18343 downstream)																																			---	---	---	---
RUNX1T1	862	broad.mit.edu	37	8	93073151	93073154	+	Intron	DEL	GAGA	-	-	rs35094638		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93073151_93073154delGAGA	uc003yfd.2	-						RUNX1T1_uc003yfc.1_Intron|RUNX1T1_uc003yfe.1_Intron|RUNX1T1_uc010mao.2_Intron|RUNX1T1_uc011lgi.1_Intron|RUNX1T1_uc003yfh.1_Intron	NM_175634	NP_783552			acute myelogenous leukemia 1 translocation 1						generation of precursor metabolites and energy	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(9)|large_intestine(3)|breast(2)|central_nervous_system(1)|pancreas(1)	16			BRCA - Breast invasive adenocarcinoma(11;0.0141)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	93342538	93342538	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93342538delT								RUNX1T1 (234832 upstream) : C8orf83 (553327 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	93444499	93444499	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93444499delC								RUNX1T1 (336793 upstream) : C8orf83 (451366 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	93501113	93501117	+	IGR	DEL	CAAAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93501113_93501117delCAAAA								RUNX1T1 (393407 upstream) : C8orf83 (394748 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	93872675	93872676	+	Intron	DEL	AC	-	-	rs34010842		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93872675_93872676delAC	uc003yfj.1	-											Homo sapiens cDNA FLJ46284 fis, clone TESTI4031818.																														---	---	---	---
FAM92A1	137392	broad.mit.edu	37	8	94730893	94730893	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94730893delT	uc010maq.2	+						FAM92A1_uc003yfv.3_Intron|FAM92A1_uc003yfx.3_Intron|FAM92A1_uc003yfw.3_Intron|FAM92A1_uc010mar.2_Intron	NM_145269	NP_660312			hypothetical protein LOC137392												0	Breast(36;2.4e-06)		BRCA - Breast invasive adenocarcinoma(8;0.0168)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	94830766	94830766	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94830766delT								TMEM67 (420 upstream) : PDP1 (98317 downstream)																																			---	---	---	---
PDP1	54704	broad.mit.edu	37	8	94937550	94937552	+	3'UTR	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94937550_94937552delTTT	uc003yge.2	+	2					PDP1_uc003ygf.2_3'UTR|PDP1_uc010max.2_3'UTR|PDP1_uc011lgm.1_3'UTR|PDP1_uc011lgn.1_3'UTR	NM_018444	NP_060914			pyruvate dehyrogenase phosphatase catalytic						pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix|protein serine/threonine phosphatase complex	[pyruvate dehydrogenase (lipoamide)] phosphatase activity			ovary(1)|skin(1)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	95036617	95036617	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95036617delG								PDP1 (98323 upstream) : CDH17 (102777 downstream)																																			---	---	---	---
CDH17	1015	broad.mit.edu	37	8	95149929	95149930	+	Intron	INS	-	A	A	rs146897711	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95149929_95149930insA	uc003ygh.2	-						CDH17_uc011lgo.1_Intron|CDH17_uc011lgp.1_Intron	NM_004063	NP_004054			cadherin 17 precursor							integral to membrane	calcium ion binding			ovary(5)|skin(1)	6	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	95331331	95331332	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95331331_95331332delTC								GEM (56774 upstream) : RAD54B (52857 downstream)																																			---	---	---	---
DPY19L4	286148	broad.mit.edu	37	8	95768113	95768113	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95768113delA	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	95779107	95779107	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95779107delA	uc003ygx.2	+							NM_181787	NP_861452			dpy-19-like 4							integral to membrane				ovary(2)	2	Breast(36;3.85e-06)																	---	---	---	---
INTS8	55656	broad.mit.edu	37	8	95834697	95834697	+	5'Flank	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95834697delA	uc003yhb.2	+						INTS8_uc003yha.1_5'Flank|INTS8_uc011lgq.1_5'Flank|INTS8_uc011lgr.1_5'Flank	NM_017864	NP_060334			integrator complex subunit 8						snRNA processing	integrator complex	protein binding				0	Breast(36;1.05e-06)																	---	---	---	---
INTS8	55656	broad.mit.edu	37	8	95884379	95884379	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95884379delT	uc003yhb.2	+						INTS8_uc011lgq.1_Intron|INTS8_uc011lgr.1_Intron|INTS8_uc010mba.2_Intron	NM_017864	NP_060334			integrator complex subunit 8						snRNA processing	integrator complex	protein binding				0	Breast(36;1.05e-06)																	---	---	---	---
Unknown	0	broad.mit.edu	37	8	96091200	96091200	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96091200delT								C8orf38 (2804 upstream) : PLEKHF2 (54838 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	96177416	96177416	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96177416delT								PLEKHF2 (8505 upstream) : C8orf37 (80819 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	96727538	96727538	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96727538delT								C8orf37 (446101 upstream) : GDF6 (427022 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	96892366	96892366	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96892366delA								C8orf37 (610929 upstream) : GDF6 (262194 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	96946738	96946738	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96946738delT								C8orf37 (665301 upstream) : GDF6 (207822 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	96975014	96975014	+	IGR	DEL	T	-	-	rs79524438		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96975014delT								C8orf37 (693577 upstream) : GDF6 (179546 downstream)																																			---	---	---	---
PTDSS1	9791	broad.mit.edu	37	8	97300562	97300562	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97300562delT	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	97411128	97411129	+	IGR	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97411128_97411129delCT								PTDSS1 (64354 upstream) : SDC2 (94753 downstream)																																			---	---	---	---
SDC2	6383	broad.mit.edu	37	8	97533095	97533095	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97533095delT	uc003yhv.1	+							NM_002998	NP_002989			syndecan 2 precursor							integral to plasma membrane	cytoskeletal protein binding|PDZ domain binding			ovary(2)	2	Breast(36;3.41e-05)				Sargramostim(DB00020)													---	---	---	---
PGCP	10404	broad.mit.edu	37	8	97825127	97825127	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97825127delA	uc003yhw.2	+						PGCP_uc010mbe.2_Intron	NM_016134	NP_057218			plasma glutamate carboxypeptidase precursor						peptide metabolic process|proteolysis	cytoplasm|extracellular space	metal ion binding|metallocarboxypeptidase activity			upper_aerodigestive_tract(1)	1	Breast(36;1.86e-05)																	---	---	---	---
PGCP	10404	broad.mit.edu	37	8	97920336	97920343	+	Intron	DEL	GTGTGTGT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97920336_97920343delGTGTGTGT	uc003yhw.2	+						PGCP_uc010mbe.2_Intron	NM_016134	NP_057218			plasma glutamate carboxypeptidase precursor						peptide metabolic process|proteolysis	cytoplasm|extracellular space	metal ion binding|metallocarboxypeptidase activity			upper_aerodigestive_tract(1)	1	Breast(36;1.86e-05)																	---	---	---	---
PGCP	10404	broad.mit.edu	37	8	98094611	98094612	+	Intron	INS	-	A	A	rs143604074	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98094611_98094612insA	uc003yhw.2	+							NM_016134	NP_057218			plasma glutamate carboxypeptidase precursor						peptide metabolic process|proteolysis	cytoplasm|extracellular space	metal ion binding|metallocarboxypeptidase activity			upper_aerodigestive_tract(1)	1	Breast(36;1.86e-05)																	---	---	---	---
PGCP	10404	broad.mit.edu	37	8	98147536	98147536	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98147536delT	uc003yhw.2	+							NM_016134	NP_057218			plasma glutamate carboxypeptidase precursor						peptide metabolic process|proteolysis	cytoplasm|extracellular space	metal ion binding|metallocarboxypeptidase activity			upper_aerodigestive_tract(1)	1	Breast(36;1.86e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	8	98294553	98294553	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98294553delA								TSPYL5 (4377 upstream) : MTDH (361854 downstream)																																			---	---	---	---
MTDH	92140	broad.mit.edu	37	8	98703932	98703933	+	Intron	DEL	TG	-	-	rs79593148		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98703932_98703933delTG	uc003yhz.2	+						MTDH_uc010mbf.2_Intron	NM_178812	NP_848927			metadherin						lipopolysaccharide-mediated signaling pathway|negative regulation of apoptosis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of angiogenesis|positive regulation of autophagy|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of protein kinase B signaling cascade	apical plasma membrane|endoplasmic reticulum membrane|integral to membrane|intercellular canaliculus|nuclear body|nuclear membrane|nucleolus|perinuclear region of cytoplasm|tight junction	NF-kappaB binding|RNA polymerase II transcription factor binding|transcription coactivator activity			liver(1)|central_nervous_system(1)	2	Breast(36;2.56e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.178)															---	---	---	---
LAPTM4B	55353	broad.mit.edu	37	8	98862694	98862695	+	Intron	DEL	GT	-	-	rs68139766		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98862694_98862695delGT	uc003yia.2	+						LAPTM4B_uc010mbg.2_Intron	NM_018407	NP_060877			lysosomal associated transmembrane protein 4						transport	endomembrane system|integral to membrane	protein binding			skin(1)	1	Breast(36;1.59e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.149)															---	---	---	---
RPL30	6156	broad.mit.edu	37	8	99054504	99054504	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99054504delT	uc003yif.2	-						RPL30_uc010mbk.1_Intron|SNORA72_uc003yig.1_5'Flank	NM_000989	NP_000980			ribosomal protein L30						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	RNA binding|structural constituent of ribosome				0	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.192)															---	---	---	---
NIPAL2	79815	broad.mit.edu	37	8	99217707	99217708	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99217707_99217708delTT	uc003yil.1	-						NIPAL2_uc011lgw.1_Intron|NIPAL2_uc003yim.1_Intron	NM_024759	NP_079035			NIPA-like domain containing 2							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	99387902	99387902	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99387902delT								NIPAL2 (81281 upstream) : KCNS2 (51348 downstream)																																			---	---	---	---
STK3	6788	broad.mit.edu	37	8	99706584	99706584	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99706584delT	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	99779079	99779079	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99779079delG	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	99792890	99792891	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99792890_99792891delAA	uc003yip.2	-						STK3_uc003yio.2_Intron|STK3_uc010mbm.1_Intron	NM_006281	NP_006272			serine/threonine kinase 3						apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)														---	---	---	---
VPS13B	157680	broad.mit.edu	37	8	100394225	100394225	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100394225delT	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	100659363	100659363	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100659363delA	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	100703476	100703477	+	Intron	DEL	TG	-	-	rs144300139		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100703476_100703477delTG	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	100865644	100865644	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100865644delG	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	100942339	100942339	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100942339delA								COX6C (36444 upstream) : RGS22 (30937 downstream)																																			---	---	---	---
RGS22	26166	broad.mit.edu	37	8	101019159	101019159	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101019159delT	uc003yjb.1	-						RGS22_uc003yja.1_Intron|RGS22_uc003yjc.1_Intron|RGS22_uc011lgz.1_Intron	NM_015668	NP_056483			regulator of G-protein signaling 22						negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity			ovary(3)|skin(2)|breast(1)|central_nervous_system(1)	7			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	101422747	101422747	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101422747delA								RNF19A (100420 upstream) : ANKRD46 (99240 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	101461708	101461710	+	IGR	DEL	GCT	-	-	rs34823749		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101461708_101461710delGCT								RNF19A (139381 upstream) : ANKRD46 (60277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	101853747	101853748	+	IGR	INS	-	TG	TG	rs147582786	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101853747_101853748insTG								PABPC1 (119432 upstream) : YWHAZ (77056 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	102008288	102008289	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102008288_102008289delTG								YWHAZ (42665 upstream) : ZNF706 (200979 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	102114027	102114027	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102114027delT								YWHAZ (148404 upstream) : ZNF706 (95241 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	102182277	102182277	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102182277delT								YWHAZ (216654 upstream) : ZNF706 (26991 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	102292273	102292273	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102292273delC								ZNF706 (74313 upstream) : NACAP1 (81749 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	102311678	102311678	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102311678delA								ZNF706 (93718 upstream) : NACAP1 (62344 downstream)																																			---	---	---	---
GRHL2	79977	broad.mit.edu	37	8	102517243	102517243	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102517243delA	uc010mbu.2	+						GRHL2_uc010mbt.1_Intron|GRHL2_uc011lhi.1_Intron	NM_024915	NP_079191			transcription factor CP2-like 3							cytoplasm|nucleus	DNA binding			ovary(2)|skin(1)	3	all_cancers(14;4.39e-08)|all_epithelial(15;4.09e-10)|Lung NSC(17;7.11e-06)|all_lung(17;1.44e-05)		Epithelial(11;5.81e-09)|all cancers(13;3.81e-07)|OV - Ovarian serous cystadenocarcinoma(57;0.000213)															---	---	---	---
GRHL2	79977	broad.mit.edu	37	8	102550665	102550665	+	Intron	DEL	A	-	-	rs79252059		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102550665delA	uc010mbu.2	+						GRHL2_uc010mbt.1_Intron|GRHL2_uc011lhi.1_Intron	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	102859464	102859464	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102859464delT	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	103495558	103495558	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103495558delT								UBR5 (71063 upstream) : ODF1 (68290 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	103807218	103807218	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103807218delA								KLF10 (139235 upstream) : AZIN1 (31319 downstream)																																			---	---	---	---
AZIN1	51582	broad.mit.edu	37	8	103863931	103863932	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103863931_103863932insA	uc003ykx.2	-						AZIN1_uc003yky.2_Intron	NM_015878	NP_056962			ornithine decarboxylase antizyme inhibitor						polyamine biosynthetic process|regulation of cellular amino acid metabolic process	cytosol	catalytic activity|protein binding				0	Lung NSC(17;0.000143)|all_lung(17;0.000294)		OV - Ovarian serous cystadenocarcinoma(57;0.000196)|STAD - Stomach adenocarcinoma(118;0.0414)															---	---	---	---
ATP6V1C1	528	broad.mit.edu	37	8	104030447	104030447	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104030447delT	uc003ykz.3	+						ATP6V1C1_uc010mbz.2_5'Flank|ATP6V1C1_uc003yla.2_5'Flank|ATP6V1C1_uc011lhl.1_5'Flank	NM_001695	NP_001686			ATPase, H+ transporting, lysosomal V1 subunit						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|plasma membrane|proton-transporting V-type ATPase, V1 domain	protein binding|proton-transporting ATPase activity, rotational mechanism				0	Lung NSC(17;0.000427)|all_lung(17;0.000533)		OV - Ovarian serous cystadenocarcinoma(57;3.57e-05)|STAD - Stomach adenocarcinoma(118;0.133)															---	---	---	---
ATP6V1C1	528	broad.mit.edu	37	8	104079208	104079208	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104079208delA	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	104436252	104436254	+	Intron	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104436252_104436254delTTT	uc003yln.2	+						DCAF13_uc003ylm.1_Intron|DCAF13_uc003ylo.2_Intron	NM_015420	NP_056235			WD repeats and SOF1 domain containing						rRNA processing	CUL4 RING ubiquitin ligase complex|nucleolus|ribonucleoprotein complex				breast(1)	1																		---	---	---	---
RIMS2	9699	broad.mit.edu	37	8	104535378	104535379	+	Intron	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104535378_104535379delAG	uc003ylp.2	+							NM_001100117	NP_001093587			regulating synaptic membrane exocytosis 2						intracellular protein transport	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	15			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)												HNSCC(12;0.0054)			---	---	---	---
RIMS2	9699	broad.mit.edu	37	8	104964310	104964311	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104964310_104964311insA	uc003yls.2	+						RIMS2_uc003ylp.2_Intron|RIMS2_uc003ylw.2_Intron|RIMS2_uc003ylq.2_Intron|RIMS2_uc003ylr.2_Intron|RIMS2_uc003ylt.2_Intron	NM_014677	NP_055492			regulating synaptic membrane exocytosis 2						intracellular protein transport	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	15			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)												HNSCC(12;0.0054)			---	---	---	---
Unknown	0	broad.mit.edu	37	8	105808353	105808353	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105808353delA								LRP12 (207133 upstream) : ZFPM2 (522794 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	105963400	105963400	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105963400delT								LRP12 (362180 upstream) : ZFPM2 (367747 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	106224492	106224496	+	IGR	DEL	TTTTT	-	-	rs7463834		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106224492_106224496delTTTTT								LRP12 (623272 upstream) : ZFPM2 (106651 downstream)																																			---	---	---	---
ZFPM2	23414	broad.mit.edu	37	8	106490949	106490949	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106490949delT	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	106705354	106705354	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106705354delA	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	106933292	106933292	+	IGR	DEL	A	-	-	rs76532396		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106933292delA								ZFPM2 (116527 upstream) : OXR1 (349181 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	107116834	107116834	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107116834delA								ZFPM2 (300069 upstream) : OXR1 (165639 downstream)																																			---	---	---	---
OXR1	55074	broad.mit.edu	37	8	107629657	107629657	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107629657delA	uc011lht.1	+						OXR1_uc003ymf.2_Intron|OXR1_uc003ymg.1_5'Flank	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	107862852	107862852	+	IGR	DEL	T	-	-	rs71825783		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107862852delT								ABRA (80380 upstream) : ANGPT1 (398859 downstream)																																			---	---	---	---
ANGPT1	284	broad.mit.edu	37	8	108448307	108448307	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108448307delT	uc003ymn.2	-						ANGPT1_uc003ymo.2_Intron	NM_001146	NP_001137			angiopoietin 1 precursor						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|blood coagulation|cell differentiation|heparin biosynthetic process|leukocyte migration|negative regulation of cell adhesion|negative regulation of endothelial cell apoptosis|negative regulation of vascular permeability|positive chemotaxis|positive regulation of blood vessel endothelial cell migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of protein ubiquitination|positive regulation of receptor internalization|protein localization at cell surface|regulation of satellite cell proliferation|sprouting angiogenesis|Tie receptor signaling pathway	extracellular space|membrane raft|microvillus|plasma membrane	receptor tyrosine kinase binding			ovary(3)|skin(3)|upper_aerodigestive_tract(1)	7	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	108859173	108859174	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108859173_108859174delTT								ANGPT1 (348919 upstream) : RSPO2 (52371 downstream)																																			---	---	---	---
RSPO2	340419	broad.mit.edu	37	8	109001191	109001191	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109001191delT	uc003yms.2	-						RSPO2_uc003ymq.2_Intron|RSPO2_uc003ymr.2_Intron	NM_178565	NP_848660			R-spondin family, member 2 precursor						Wnt receptor signaling pathway	extracellular region	heparin binding			skin(3)|ovary(2)|pancreas(1)|lung(1)	7			OV - Ovarian serous cystadenocarcinoma(57;1.55e-09)															---	---	---	---
RSPO2	340419	broad.mit.edu	37	8	109087709	109087709	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109087709delA	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	109147853	109147853	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109147853delT								RSPO2 (51940 upstream) : EIF3E (66120 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	109612368	109612368	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109612368delT								TTC35 (113232 upstream) : TMEM74 (6712 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	109936054	109936054	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109936054delG								TMEM74 (136284 upstream) : TRHR (163685 downstream)																																			---	---	---	---
EBAG9	9166	broad.mit.edu	37	8	110573290	110573290	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110573290delT	uc003ynf.2	+						EBAG9_uc003yng.2_Intron	NM_198120	NP_936056			estrogen receptor binding site associated						apoptosis|regulation of cell growth	focal adhesion|Golgi membrane|integral to membrane|soluble fraction	apoptotic protease activator activity				0			OV - Ovarian serous cystadenocarcinoma(57;1.39e-14)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	110964705	110964705	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110964705delT								SYBU (260685 upstream) : KCNV1 (14530 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	111526142	111526142	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111526142delT								KCNV1 (538066 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	111642062	111642062	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111642062delT								KCNV1 (653986 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	112535192	112535192	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112535192delT								None (None upstream) : CSMD3 (699969 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	112899521	112899524	+	IGR	DEL	TGTG	-	-	rs72351432		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112899521_112899524delTGTG								None (None upstream) : CSMD3 (335637 downstream)																																			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113268532	113268532	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113268532delA	uc003ynu.2	-						CSMD3_uc003yns.2_Intron|CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756			CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113421012	113421012	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113421012delA	uc003ynu.2	-						CSMD3_uc003yns.2_Intron|CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756			CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113486125	113486125	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113486125delT	uc003ynu.2	-						CSMD3_uc003yns.2_Intron|CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756			CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113540691	113540691	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113540691delA	uc003ynu.2	-						CSMD3_uc003yns.2_Intron|CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756			CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113582536	113582536	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113582536delA	uc003ynu.2	-						CSMD3_uc003yns.2_Intron|CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756			CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113648768	113648771	+	Intron	DEL	TCTA	-	-	rs66467010		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113648768_113648771delTCTA	uc003ynu.2	-						CSMD3_uc003yns.2_Intron|CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756			CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	114183236	114183237	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114183236_114183237delAA	uc003ynu.2	-						CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron|CSMD3_uc010mcx.1_Intron	NM_198123	NP_937756			CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	114443945	114443945	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114443945delT	uc003ynu.2	-						CSMD3_uc011lhx.1_Intron|CSMD3_uc010mcx.1_Intron|CSMD3_uc003ynx.3_Intron	NM_198123	NP_937756			CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
Unknown	0	broad.mit.edu	37	8	114510481	114510481	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114510481delT								CSMD3 (61239 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	114818765	114818765	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114818765delA								CSMD3 (369523 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	115778583	115778583	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:115778583delA								None (None upstream) : TRPS1 (642142 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116010907	116010907	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116010907delT								None (None upstream) : TRPS1 (409818 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116119849	116119849	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116119849delC								None (None upstream) : TRPS1 (300876 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116124997	116125000	+	IGR	DEL	ACAC	-	-	rs147416128		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116124997_116125000delACAC								None (None upstream) : TRPS1 (295725 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116372053	116372053	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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	116410661	116410661	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116410661delT								None (None upstream) : TRPS1 (10064 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116779854	116779854	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116779854delT								TRPS1 (98626 upstream) : EIF3H (877202 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116834265	116834266	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116834265_116834266delTG								TRPS1 (153037 upstream) : EIF3H (822790 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116855021	116855021	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116855021delA								TRPS1 (173793 upstream) : EIF3H (802035 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116857315	116857315	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116857315delA								TRPS1 (176087 upstream) : EIF3H (799741 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117007024	117007024	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117007024delA								TRPS1 (325796 upstream) : EIF3H (650032 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117549752	117549752	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117549752delA								TRPS1 (868524 upstream) : EIF3H (107304 downstream)																																			---	---	---	---
EIF3H	8667	broad.mit.edu	37	8	117740011	117740011	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117740011delA	uc003yoa.2	-						EIF3H_uc003yob.2_Intron|EIF3H_uc011lhz.1_Intron	NM_003756	NP_003747			eukaryotic translation initiation factor 3,						regulation of translational initiation	cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			lung(3)	3	all_cancers(13;3.98e-22)|Lung NSC(37;0.000183)|Ovarian(258;0.0172)																	---	---	---	---
Unknown	0	broad.mit.edu	37	8	117935376	117935379	+	IGR	DEL	TTTT	-	-	rs66582668		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117935376_117935379delTTTT								RAD21 (48271 upstream) : C8orf85 (15085 downstream)																																			---	---	---	---
SLC30A8	169026	broad.mit.edu	37	8	118079595	118079596	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118079595_118079596delTT	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	118738041	118738042	+	IGR	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118738041_118738042delCT								MED30 (185542 upstream) : EXT1 (73560 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	118761224	118761224	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118761224delT								MED30 (208725 upstream) : EXT1 (50378 downstream)																																			---	---	---	---
EXT1	2131	broad.mit.edu	37	8	118820106	118820106	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118820106delA	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	119115393	119115393	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119115393delA	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	120027064	120027064	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120027064delT								TNFRSF11B (62681 upstream) : COLEC10 (52360 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	120188536	120188537	+	IGR	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120188536_120188537delGT								COLEC10 (69341 upstream) : MAL2 (32073 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	120193228	120193228	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120193228delT								COLEC10 (74033 upstream) : MAL2 (27382 downstream)																																			---	---	---	---
ENPP2	5168	broad.mit.edu	37	8	120642354	120642355	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120642354_120642355delTT	uc003yot.1	-						ENPP2_uc003yos.1_Intron|ENPP2_uc010mdd.1_Intron	NM_001040092	NP_001035181			autotaxin isoform 2 preproprotein						cellular component movement|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|phosphate metabolic process|phosphatidylcholine catabolic process|regulation of cell migration	extracellular space|integral to plasma membrane	alkylglycerophosphoethanolamine phosphodiesterase activity|calcium ion binding|lysophospholipase activity|nucleic acid binding|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity|transcription factor binding|zinc ion binding			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|large_intestine(1)|kidney(1)	7	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	120872062	120872063	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120872062_120872063delTC								DSCC1 (3892 upstream) : DEPDC6 (13837 downstream)																																			---	---	---	---
DEPDC6	64798	broad.mit.edu	37	8	121024311	121024311	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121024311delA	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)															---	---	---	---
SNTB1	6641	broad.mit.edu	37	8	121716696	121716696	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121716696delA	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	122625187	122625188	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122625187_122625188delAA								SNTB1 (800878 upstream) : HAS2 (83 downstream)																																			---	---	---	---
HAS2	3037	broad.mit.edu	37	8	122640781	122640781	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122640781delT	uc003yph.2	-							NM_005328	NP_005319			hyaluronan synthase 2							integral to plasma membrane	hyaluronan synthase activity		HAS2/PLAG1(10)	soft_tissue(10)|ovary(5)	15	Lung NSC(37;3.12e-08)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)|all_neural(195;0.142)		STAD - Stomach adenocarcinoma(47;0.00503)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	122741171	122741171	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122741171delT								HAS2AS (84238 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123436737	123436737	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123436737delT								HAS2AS (779804 upstream) : ZHX2 (357164 downstream)																																			---	---	---	---
ZHX2	22882	broad.mit.edu	37	8	123811041	123811041	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123811041delA	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)															---	---	---	---
ZHX2	22882	broad.mit.edu	37	8	123949128	123949128	+	Intron	DEL	C	-	-	rs5894649		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123949128delC	uc003ypk.1	+							NM_014943	NP_055758			zinc fingers and homeoboxes 2							cytoplasm|nucleus|plasma membrane	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)															---	---	---	---
WDR67	93594	broad.mit.edu	37	8	124098959	124098959	+	Intron	DEL	T	-	-	rs112065086		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124098959delT	uc003ypp.1	+						WDR67_uc011lig.1_Intron|WDR67_uc011lih.1_Intron|WDR67_uc003ypq.1_Intron|WDR67_uc003ypo.1_Intron	NM_145647	NP_663622			WD repeat domain 67 isoform 1							centrosome	Rab GTPase activator activity			skin(1)	1	Lung NSC(37;7e-10)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	124228191	124228191	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124228191delA								FAM83A (5874 upstream) : C8orf76 (4040 downstream)																																			---	---	---	---
ZHX1	11244	broad.mit.edu	37	8	124275174	124275174	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124275174delA	uc003yqe.2	-						C8orf76_uc003yqd.2_Intron|ZHX1_uc003yqf.2_Intron|ZHX1_uc003yqg.2_Intron|ZHX1_uc010mdi.2_Intron	NM_007222	NP_009153			zinc fingers and homeoboxes 1						negative regulation of transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)															---	---	---	---
ATAD2	29028	broad.mit.edu	37	8	124353188	124353190	+	Intron	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124353188_124353190delTTT	uc003yqh.3	-						ATAD2_uc011lii.1_Intron|ATAD2_uc003yqi.3_Intron	NM_014109	NP_054828			ATPase family, AAA domain containing 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrion|nucleus	ATP binding|ATPase activity			ovary(2)	2	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	124762858	124762858	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124762858delT								ANXA13 (13211 upstream) : FAM91A1 (18024 downstream)																																			---	---	---	---
FER1L6	654463	broad.mit.edu	37	8	124897230	124897230	+	Intron	DEL	A	-	-	rs146425959	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124897230delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	125148835	125148835	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125148835delT	uc003yqy.1	-											Homo sapiens cDNA FLJ32770 fis, clone TESTI2001898.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	125298711	125298712	+	IGR	INS	-	TCTC	TCTC	rs141379773	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125298711_125298712insTCTC								FER1L6 (166410 upstream) : TMEM65 (24449 downstream)																																			---	---	---	---
TMEM65	157378	broad.mit.edu	37	8	125378770	125378770	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125378770delT	uc010mdl.2	-							NM_194291	NP_919267			transmembrane protein 65							integral to membrane					0	Lung NSC(37;1.18e-11)|Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	125981594	125981594	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125981594delA								LOC157381 (18257 upstream) : ZNF572 (3945 downstream)																																			---	---	---	---
SQLE	6713	broad.mit.edu	37	8	126013692	126013695	+	Intron	DEL	GTGT	-	-	rs67020956		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126013692_126013695delGTGT	uc011liq.1	+							NM_003129	NP_003120			squalene epoxidase						cholesterol biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome	flavin adenine dinucleotide binding|squalene monooxygenase activity			ovary(1)|breast(1)	2	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)		Butenafine(DB01091)|Naftifine(DB00735)|Terbinafine(DB00857)													---	---	---	---
KIAA0196	9897	broad.mit.edu	37	8	126095506	126095506	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126095506delA	uc003yrt.2	-						KIAA0196_uc011lir.1_Intron	NM_014846	NP_055661			strumpellin						cell death	WASH complex				ovary(2)	2	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)															---	---	---	---
NSMCE2	286053	broad.mit.edu	37	8	126304463	126304464	+	Intron	DEL	AA	-	-	rs34130712		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126304463_126304464delAA	uc003yrw.2	+							NM_173685	NP_775956			non-SMC element 2, MMS21 homolog						DNA recombination|DNA repair	nucleus	ligase activity|zinc ion binding			breast(1)	1	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	126503972	126503972	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126503972delA								TRIB1 (53330 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	126815853	126815854	+	IGR	INS	-	C	C	rs139780014	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126815853_126815854insC								TRIB1 (365211 upstream) : FAM84B (748833 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127130818	127130819	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127130818_127130819insT								TRIB1 (680176 upstream) : FAM84B (433868 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127174996	127174996	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127174996delA								TRIB1 (724354 upstream) : FAM84B (389691 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127273974	127273974	+	IGR	DEL	A	-	-	rs144754290		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127273974delA								TRIB1 (823332 upstream) : FAM84B (290713 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127344004	127344004	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127344004delT								TRIB1 (893362 upstream) : FAM84B (220683 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	128115077	128115078	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128115077_128115078delAC								FAM84B (544611 upstream) : LOC727677 (186984 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	128180907	128180908	+	IGR	INS	-	T	T	rs2456457	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128180907_128180908insT								FAM84B (610441 upstream) : LOC727677 (121154 downstream)																																			---	---	---	---
LOC727677	727677	broad.mit.edu	37	8	128484188	128484188	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128484188delA	uc003yse.1	-						LOC727677_uc011liv.1_Intron					Homo sapiens isolate DGPc1_8_exons1-2-3-4-5 unknown mRNA, alternatively spliced.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	128574529	128574530	+	IGR	DEL	CA	-	-	rs113761762		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128574529_128574530delCA								LOC727677 (80145 upstream) : MYC (173235 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	128798440	128798440	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128798440delT								MYC (44762 upstream) : PVT1 (8339 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	129166766	129166766	+	IGR	DEL	T	-	-	rs34769615		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129166766delT								MIR1208 (4332 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	129180201	129180201	+	IGR	DEL	C	-	-	rs72196366		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129180201delC								MIR1208 (17767 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	129614198	129614199	+	IGR	DEL	CA	-	-	rs148905849		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129614198_129614199delCA								MIR1208 (451764 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	129702329	129702336	+	IGR	DEL	TTTTTTTC	-	-	rs74383763		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129702329_129702336delTTTTTTTC								MIR1208 (539895 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	129899254	129899255	+	IGR	DEL	GA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129899254_129899255delGA								MIR1208 (736820 upstream) : GSDMC (861188 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	130193941	130193941	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130193941delT								None (None upstream) : GSDMC (566502 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	130263601	130263602	+	IGR	INS	-	A	A	rs5894980		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130263601_130263602insA								None (None upstream) : GSDMC (496841 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	130587025	130587026	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130587025_130587026delTC								None (None upstream) : GSDMC (173417 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	130709483	130709485	+	IGR	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130709483_130709485delTTT								None (None upstream) : GSDMC (50958 downstream)																																			---	---	---	---
FAM49B	51571	broad.mit.edu	37	8	130997893	130997893	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130997893delA	uc003ysw.2	-						FAM49B_uc003ysx.2_Intron|FAM49B_uc003ysy.1_Intron	NM_016623	NP_057707			hypothetical protein LOC51571												0	Ovarian(5;0.000567)|Esophageal squamous(12;0.00693)|Acute lymphoblastic leukemia(118;0.155)		LUAD - Lung adenocarcinoma(14;0.0989)															---	---	---	---
ASAP1	50807	broad.mit.edu	37	8	131140419	131140420	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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	131259773	131259773	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131259773delA	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																		---	---	---	---
ADCY8	114	broad.mit.edu	37	8	131858967	131858968	+	Intron	INS	-	CCTT	CCTT	rs151049495	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131858967_131858968insCCTT	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	131877924	131877924	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131877924delT	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	131882265	131882266	+	Intron	DEL	TT	-	-	rs78803578		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131882265_131882266delTT	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	132150164	132150164	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132150164delT								ADCY8 (97329 upstream) : EFR3A (766195 downstream)																																			---	---	---	---
KCNQ3	3786	broad.mit.edu	37	8	133163082	133163083	+	Intron	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133163082_133163083delTG	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	133312484	133312484	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133312484delT	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	133440772	133440773	+	Intron	INS	-	CA	CA			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133440772_133440773insCA	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	133874028	133874028	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133874028delT								PHF20L1 (12978 upstream) : TG (5177 downstream)																																			---	---	---	---
NDRG1	10397	broad.mit.edu	37	8	134262922	134262922	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134262922delA	uc003yuh.2	-						NDRG1_uc003yuf.1_Intron|NDRG1_uc003yug.2_Intron|NDRG1_uc010mee.2_Intron|NDRG1_uc010mef.2_Intron|NDRG1_uc011ljh.1_Intron|NDRG1_uc011lji.1_Intron	NM_001135242	NP_001128714			N-myc downstream regulated 1						cellular response to hypoxia|response to metal ion	cytoplasm|microtubule cytoskeleton|nucleus|plasma membrane	protein binding			ovary(4)	4	all_epithelial(106;4.26e-24)|Lung NSC(106;7.26e-07)|all_lung(105;2.77e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0107)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	134352439	134352440	+	IGR	DEL	GT	-	-	rs35004481		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134352439_134352440delGT								NDRG1 (42892 upstream) : ST3GAL1 (114651 downstream)																																			---	---	---	---
ST3GAL1	6482	broad.mit.edu	37	8	134568110	134568110	+	Intron	DEL	G	-	-	rs10101555	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134568110delG	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	135315940	135315941	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135315940_135315941insT								ST3GAL1 (731757 upstream) : ZFAT (174092 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	135468763	135468764	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135468763_135468764delTG								ST3GAL1 (884580 upstream) : ZFAT (21269 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	135929663	135929663	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135929663delT								MIR30D (112475 upstream) : LOC286094 (316711 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	136675141	136675142	+	IGR	DEL	CG	-	-	rs72169409	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136675141_136675142delCG								KHDRBS3 (15295 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	136707736	136707736	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136707736delT								KHDRBS3 (47890 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	136869363	136869364	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136869363_136869364delAC								KHDRBS3 (209517 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	137173548	137173548	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137173548delA								KHDRBS3 (513702 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	137198048	137198048	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137198048delA								KHDRBS3 (538202 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	137279627	137279628	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137279627_137279628delTC								KHDRBS3 (619781 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	137394998	137394998	+	IGR	DEL	T	-	-	rs112760994		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137394998delT								KHDRBS3 (735152 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	137576415	137576415	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137576415delA								KHDRBS3 (916569 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	137713917	137713918	+	IGR	INS	-	T	T	rs150275257	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137713917_137713918insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	137715741	137715741	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137715741delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	137815540	137815541	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137815540_137815541delTG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138136471	138136471	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138136471delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138443332	138443332	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138443332delA								None (None upstream) : FAM135B (698936 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138548747	138548747	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138548747delA								None (None upstream) : FAM135B (593521 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138625898	138625898	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138625898delA								None (None upstream) : FAM135B (516370 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138778226	138778227	+	IGR	INS	-	TC	TC	rs138729873	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138778226_138778227insTC								None (None upstream) : FAM135B (364041 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	139032202	139032203	+	IGR	DEL	TT	-	-	rs79269146		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139032202_139032203delTT								None (None upstream) : FAM135B (110065 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	139102168	139102169	+	IGR	INS	-	C	C	rs72541572	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139102168_139102169insC								None (None upstream) : FAM135B (40099 downstream)																																			---	---	---	---
COL22A1	169044	broad.mit.edu	37	8	139727812	139727820	+	Intron	DEL	TAAAAAAAA	-	-	rs143920292		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139727812_139727820delTAAAAAAAA	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	139757434	139757434	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139757434delT	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)			---	---	---	---
Unknown	0	broad.mit.edu	37	8	139953421	139953422	+	IGR	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139953421_139953422delGT								COL22A1 (27185 upstream) : KCNK9 (659660 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	140005454	140005455	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140005454_140005455delAA								COL22A1 (79218 upstream) : KCNK9 (607627 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	140130703	140130703	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140130703delA								COL22A1 (204467 upstream) : KCNK9 (482379 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	140740269	140740269	+	IGR	DEL	A	-	-	rs112910648		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140740269delA								KCNK9 (24970 upstream) : TRAPPC9 (2317 downstream)																																			---	---	---	---
TRAPPC9	83696	broad.mit.edu	37	8	140927500	140927500	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140927500delT	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																		---	---	---	---
EIF2C2	27161	broad.mit.edu	37	8	141547827	141547827	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141547827delT	uc003yvn.2	-						EIF2C2_uc010men.2_Intron|EIF2C2_uc010meo.2_Intron	NM_012154	NP_036286			argonaute 2 isoform 1						mRNA cleavage involved in gene silencing by miRNA|negative regulation of translation involved in gene silencing by miRNA|negative regulation of translational initiation|pre-miRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|micro-ribonucleoprotein complex|mRNA cap binding complex|nucleus|polysome|RNA-induced silencing complex	endoribonuclease activity, cleaving siRNA-paired mRNA|metal ion binding|protein binding|RNA 7-methylguanosine cap binding|siRNA binding|translation initiation factor activity				0	all_cancers(97;2.54e-14)|all_epithelial(106;5.99e-13)|Lung NSC(106;1.45e-05)|all_lung(105;2.07e-05)|Ovarian(258;0.0154)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.158)															---	---	---	---
PTK2	5747	broad.mit.edu	37	8	141810338	141810338	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141810338delT	uc003yvu.2	-						PTK2_uc011ljq.1_Intron|PTK2_uc003yvp.2_Intron|PTK2_uc003yvq.2_Intron|PTK2_uc003yvr.2_Intron|PTK2_uc003yvs.2_Intron|PTK2_uc003yvt.2_Intron|PTK2_uc003yvv.2_Intron|PTK2_uc011ljr.1_Intron	NM_153831	NP_722560			PTK2 protein tyrosine kinase 2 isoform a						axon guidance|blood coagulation|cellular component disassembly involved in apoptosis|ephrin receptor signaling pathway|growth hormone receptor signaling pathway|integrin-mediated signaling pathway|peptidyl-tyrosine phosphorylation|protein autophosphorylation|regulation of cell adhesion mediated by integrin|signal complex assembly	cytoskeleton|cytosol|focal adhesion	ATP binding|JUN kinase binding|non-membrane spanning protein tyrosine kinase activity|SH2 domain binding|signal transducer activity			ovary(2)|lung(2)|central_nervous_system(1)|skin(1)	6	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	142321638	142321639	+	IGR	INS	-	GT	GT	rs66919827		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142321638_142321639insGT								SLC45A4 (57413 upstream) : LOC731779 (29009 downstream)																																			---	---	---	---
FLJ43860	389690	broad.mit.edu	37	8	142457654	142457654	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142457654delA	uc003ywi.2	-						FLJ43860_uc011ljs.1_Intron|FLJ43860_uc010meu.1_Intron	NM_207414	NP_997297			hypothetical protein LOC389690								binding				0	all_cancers(97;7.79e-15)|all_epithelial(106;4.52e-13)|Lung NSC(106;2.07e-05)|all_lung(105;2.89e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)															---	---	---	---
FLJ43860	389690	broad.mit.edu	37	8	142461739	142461739	+	Intron	DEL	T	-	-	rs7829781	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142461739delT	uc003ywi.2	-						FLJ43860_uc011ljs.1_Intron|FLJ43860_uc010meu.1_Intron	NM_207414	NP_997297			hypothetical protein LOC389690								binding				0	all_cancers(97;7.79e-15)|all_epithelial(106;4.52e-13)|Lung NSC(106;2.07e-05)|all_lung(105;2.89e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	143094451	143094451	+	IGR	DEL	C	-	-	rs113650348		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143094451delC								MIR1302-7 (226777 upstream) : NCRNA00051 (185266 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	143267243	143267244	+	IGR	INS	-	CAC	CAC			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143267243_143267244insCAC								MIR1302-7 (399569 upstream) : NCRNA00051 (12473 downstream)																																			---	---	---	---
TSNARE1	203062	broad.mit.edu	37	8	143337296	143337296	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143337296delC	uc003ywk.2	-						TSNARE1_uc011lju.1_Intron|TSNARE1_uc003ywj.2_Intron	NM_145003	NP_659440			t-SNARE domain containing 1						vesicle-mediated transport	integral to membrane					0	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	8	143516278	143516279	+	IGR	INS	-	CT	CT	rs148345493	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143516278_143516279insCT								TSNARE1 (31735 upstream) : BAI1 (29098 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	143928720	143928720	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143928720delT								GML (459 upstream) : CYP11B1 (25054 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	144325487	144325487	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144325487delA								GPIHBP1 (26444 upstream) : ZFP41 (3504 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	145081848	145081848	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145081848delC								GRINA (14265 upstream) : SPATC1 (4734 downstream)																																			---	---	---	---
BOP1	23246	broad.mit.edu	37	8	145504886	145504887	+	Intron	DEL	AA	-	-	rs112319028		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145504886_145504887delAA	uc003zbr.1	-							NM_015201	NP_056016			block of proliferation 1						cell proliferation|maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|regulation of cell cycle	nucleoplasm|PeBoW complex	protein binding				0	all_cancers(97;4.06e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;2.61e-39)|all cancers(56;1.37e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.087)															---	---	---	---
ARHGAP39	80728	broad.mit.edu	37	8	145794258	145794258	+	Intron	DEL	A	-	-	rs111230522		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145794258delA	uc003zdt.1	-						ARHGAP39_uc011llk.1_Intron|ARHGAP39_uc003zds.1_Intron	NM_025251	NP_079527			KIAA1688 protein						axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytoskeleton|cytosol|nucleus	GTPase activator activity				0																		---	---	---	---
ZNF517	340385	broad.mit.edu	37	8	146032685	146032685	+	Frame_Shift_Del	DEL	G	-	-	rs113318407	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146032685delG	uc003zed.1	+	5	491	c.384delG	c.(382-384)GTGfs	p.V128fs	ZNF517_uc010mgd.1_Frame_Shift_Del_p.V34fs|ZNF517_uc003zee.1_RNA|ZNF517_uc011llm.1_Frame_Shift_Del_p.V34fs|ZNF517_uc003zef.1_Intron	NM_213605	NP_998770	Q6ZMY9	ZN517_HUMAN	zinc finger protein 517	128					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;5.47e-39)|OV - Ovarian serous cystadenocarcinoma(54;6.38e-39)|all cancers(56;5.47e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)															---	---	---	---
ZNF16	7564	broad.mit.edu	37	8	146165473	146165473	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146165473delT	uc003zet.2	-						ZNF16_uc003zeu.2_Intron	NM_001029976	NP_001025147			zinc finger protein 16						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(5)	5	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.136)	Epithelial(56;3.45e-38)|all cancers(56;3.04e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0424)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.02)|KIRC - Kidney renal clear cell carcinoma(644;0.0486)														---	---	---	---
KANK1	23189	broad.mit.edu	37	9	587151	587152	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:587151_587152insT	uc003zgl.1	+						KANK1_uc003zgm.2_Intron|KANK1_uc003zgn.1_Intron|KANK1_uc003zgo.1_Intron|KANK1_uc003zgp.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)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	1158924	1158925	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1158924_1158925delTG								DMRT2 (101371 upstream) : SMARCA2 (856417 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	1270017	1270017	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1270017delC								DMRT2 (212464 upstream) : SMARCA2 (745325 downstream)																																			---	---	---	---
SMARCA2	6595	broad.mit.edu	37	9	2101643	2101643	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2101643delA	uc003zhc.2	+						SMARCA2_uc003zhd.2_Intron|SMARCA2_uc010mha.2_Intron	NM_003070	NP_003061			SWI/SNF-related matrix-associated						chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development	intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex	ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding			ovary(2)|central_nervous_system(1)	3		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)														---	---	---	---
RFX3	5991	broad.mit.edu	37	9	3356156	3356159	+	Intron	DEL	GGAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:3356156_3356159delGGAA	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)														---	---	---	---
RFX3	5991	broad.mit.edu	37	9	3525265	3525265	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:3525265delC	uc003zhr.2	-						RFX3_uc010mhd.2_Intron|RFX3_uc003zhs.1_Intron|RFX3_uc010mhe.1_Intron	NM_134428	NP_602304			regulatory factor X3 isoform b						cell maturation|ciliary cell motility|cilium assembly|cilium movement involved in determination of left/right asymmetry|endocrine pancreas development|negative regulation of transcription, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type B pancreatic cell development|regulation of insulin secretion	nuclear chromatin	protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4				GBM - Glioblastoma multiforme(50;0.00124)|Lung(2;0.0337)														---	---	---	---
GLIS3	169792	broad.mit.edu	37	9	3937256	3937256	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:3937256delA	uc003zhw.1	-						GLIS3_uc003zhx.1_Intron|GLIS3_uc010mhf.1_5'Flank|GLIS3_uc003zhv.1_Intron|GLIS3_uc003zhy.1_Intron|GLIS3_uc003zhz.1_Intron	NM_152629	NP_689842			GLIS family zinc finger 3 isoform b						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		DNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)														---	---	---	---
GLIS3	169792	broad.mit.edu	37	9	3984137	3984137	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:3984137delC	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	4406244	4406244	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4406244delA								GLIS3 (106209 upstream) : SLC1A1 (84200 downstream)																																			---	---	---	---
SLC1A1	6505	broad.mit.edu	37	9	4559548	4559548	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4559548delA	uc003zij.1	+						C9orf68_uc003zik.2_Intron	NM_004170	NP_004161			solute carrier family 1, member 1						D-aspartate import|L-glutamate import|synaptic transmission	integral to plasma membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity				0		Acute lymphoblastic leukemia(2;0.0359)|Breast(48;0.0457)		GBM - Glioblastoma multiforme(50;0.0124)|Lung(218;0.183)	L-Aspartic Acid(DB00128)|L-Glutamic Acid(DB00142)													---	---	---	---
JAK2	3717	broad.mit.edu	37	9	5091046	5091046	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5091046delT	uc010mhm.2	+						JAK2_uc003ziw.2_Intron	NM_004972	NP_004963			Janus kinase 2						actin filament polymerization|activation of caspase activity by protein phosphorylation|activation of JAK2 kinase activity|blood coagulation|cellular component movement|erythrocyte differentiation|interferon-gamma-mediated signaling pathway|interleukin-12-mediated signaling pathway|JAK-STAT cascade involved in growth hormone signaling pathway|mammary gland epithelium development|mesoderm development|negative regulation of cell proliferation|negative regulation of DNA binding|positive regulation of apoptosis|positive regulation of cell-substrate adhesion|positive regulation of growth hormone receptor signaling pathway|positive regulation of nitric-oxide synthase 2 biosynthetic process|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of tumor necrosis factor production|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|protein autophosphorylation|regulation of inflammatory response|regulation of interferon-gamma-mediated signaling pathway|response to antibiotic|response to lipopolysaccharide|STAT protein import into nucleus|tumor necrosis factor-mediated signaling pathway|tyrosine phosphorylation of STAT protein	caveola|cytoskeleton|cytosol|endomembrane system|nucleus	ATP binding|growth hormone receptor binding|heme binding|histone binding|histone kinase activity (H3-Y41 specific)|interleukin-12 receptor binding|non-membrane spanning protein tyrosine kinase activity|protein kinase binding|SH2 domain binding		PCM1/JAK2(30)|PAX5/JAK2(18)|ETV6/JAK2(11)|BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)	haematopoietic_and_lymphoid_tissue(28629)|lung(5)|breast(5)|ovary(1)|liver(1)	28641	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)			1	T|Mis|O	ETV6|PCM1|BCR	ALL|AML|MPD| CML				Polycythemia_Vera_Familial				---	---	---	---
INSL6	11172	broad.mit.edu	37	9	5175072	5175072	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5175072delT	uc003zix.2	-							NM_007179	NP_009110			insulin-like 6 precursor							extracellular region	hormone activity				0	all_hematologic(13;0.137)	Breast(48;0.147)|Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0128)|Lung(218;0.145)														---	---	---	---
C9orf46	55848	broad.mit.edu	37	9	5432077	5432078	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5432077_5432078delAA	uc003zjc.2	-						C9orf46_uc003zjd.2_Intron	NM_018465	NP_060935			hypothetical protein LOC55848							integral to membrane				ovary(1)	1	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.00106)|Lung(218;0.125)														---	---	---	---
KIAA1432	57589	broad.mit.edu	37	9	5753519	5753519	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5753519delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	6200265	6200266	+	IGR	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6200265_6200266delCT								RANBP6 (184625 upstream) : IL33 (15541 downstream)																																			---	---	---	---
UHRF2	115426	broad.mit.edu	37	9	6411003	6411003	+	5'Flank	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6411003delA	uc003zjy.2	+						UHRF2_uc003zjz.2_5'Flank	NM_152896	NP_690856			ubiquitin-like with PHD and ring finger domains						cell cycle|cell differentiation|cell proliferation|protein autoubiquitination|regulation of cell cycle|ubiquitin-dependent protein catabolic process	nucleus	DNA binding|histone binding|ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)	3		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0392)|Lung(218;0.129)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	7289351	7289352	+	IGR	DEL	AG	-	-	rs12238025		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7289351_7289352delAG								KDM4C (113704 upstream) : C9orf123 (507141 downstream)																																			---	---	---	---
PTPRD	5789	broad.mit.edu	37	9	8501114	8501114	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8501114delA	uc003zkk.2	-						PTPRD_uc003zkp.2_Intron|PTPRD_uc003zkq.2_Intron|PTPRD_uc003zkr.2_Intron|PTPRD_uc003zks.2_Intron|PTPRD_uc003zkl.2_Intron|PTPRD_uc003zkm.2_Intron|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron	NM_002839	NP_002830			protein tyrosine phosphatase, receptor type, D						transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)											TSP Lung(15;0.13)			---	---	---	---
PTPRD	5789	broad.mit.edu	37	9	8633120	8633121	+	Intron	INS	-	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8633120_8633121insC	uc003zkk.2	-						PTPRD_uc003zkp.2_Intron|PTPRD_uc003zkq.2_Intron|PTPRD_uc003zkr.2_Intron|PTPRD_uc003zks.2_Intron|PTPRD_uc003zkl.2_Intron|PTPRD_uc003zkm.2_Intron|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron|PTPRD_uc003zkt.1_Intron	NM_002839	NP_002830			protein tyrosine phosphatase, receptor type, D						transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)											TSP Lung(15;0.13)			---	---	---	---
PTPRD	5789	broad.mit.edu	37	9	8868366	8868366	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8868366delT	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	9268984	9268984	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:9268984delA	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	9490244	9490244	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:9490244delA	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	9501111	9501111	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:9501111delA	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	9791337	9791337	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:9791337delT	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	10812806	10812807	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:10812806_10812807delAC								PTPRD (200083 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	12530854	12530855	+	IGR	INS	-	TG	TG	rs791698	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12530854_12530855insTG								None (None upstream) : TYRP1 (162531 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	14372111	14372111	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14372111delT								NFIB (58166 upstream) : ZDHHC21 (183370 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	14405720	14405720	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14405720delA								NFIB (91775 upstream) : ZDHHC21 (149761 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	14516470	14516470	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14516470delA								NFIB (202525 upstream) : ZDHHC21 (39011 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	15001532	15001532	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15001532delA	uc003zln.1	-						LOC389705_uc010mid.1_Intron					Homo sapiens cDNA FLJ46077 fis, clone TESTI2003768, weakly  similar to Chloride channel protein 3.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	15169444	15169444	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15169444delA								LOC389705 (149722 upstream) : TTC39B (2117 downstream)																																			---	---	---	---
C9orf93	203238	broad.mit.edu	37	9	15558064	15558064	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15558064delC	uc003zmd.2	+						C9orf93_uc010mih.1_Intron|C9orf93_uc003zme.2_Intron|C9orf93_uc003zmc.2_Intron	NM_173550	NP_775821			hypothetical protein LOC203238												0				GBM - Glioblastoma multiforme(50;4.84e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	16095541	16095542	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16095541_16095542delTC								C9orf93 (123646 upstream) : BNC2 (313960 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	16167318	16167318	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16167318delT								C9orf93 (195423 upstream) : BNC2 (242184 downstream)																																			---	---	---	---
SH3GL2	6456	broad.mit.edu	37	9	17601256	17601256	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17601256delT	uc003zna.2	+							NM_003026	NP_003017			SH3-domain GRB2-like 2						axon guidance|central nervous system development|endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport	cytosol|Golgi membrane|plasma membrane	identical protein binding|lipid binding			skin(1)	1				GBM - Glioblastoma multiforme(50;2.71e-10)|Lung(42;0.203)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	18258291	18258291	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18258291delA								SH3GL2 (461171 upstream) : ADAMTSL1 (215813 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	18298672	18298674	+	IGR	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18298672_18298674delAAA								SH3GL2 (501552 upstream) : ADAMTSL1 (175430 downstream)																																			---	---	---	---
ADAMTSL1	92949	broad.mit.edu	37	9	18791521	18791522	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18791521_18791522delAA	uc003zne.3	+							NM_001040272	NP_001035362			ADAMTS-like 1 isoform 4 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)	5				GBM - Glioblastoma multiforme(50;1.29e-17)														---	---	---	---
ADAMTSL1	92949	broad.mit.edu	37	9	18830071	18830071	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18830071delG	uc003zne.3	+						ADAMTSL1_uc003znf.3_Intron	NM_001040272	NP_001035362			ADAMTS-like 1 isoform 4 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)	5				GBM - Glioblastoma multiforme(50;1.29e-17)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	19204368	19204368	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19204368delT								PLIN2 (76795 upstream) : DENND4C (86334 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	19218436	19218436	+	IGR	DEL	T	-	-	rs72252306		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19218436delT								PLIN2 (90863 upstream) : DENND4C (72266 downstream)																																			---	---	---	---
ACER2	340485	broad.mit.edu	37	9	19426227	19426228	+	Intron	DEL	AA	-	-	rs116119251	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19426227_19426228delAA	uc003zny.1	+						ACER2_uc003znx.1_Intron|ACER2_uc003znz.1_Intron	NM_001010887	NP_001010887			alkaline ceramidase 2						ceramide metabolic process|negative regulation of cell adhesion mediated by integrin|negative regulation of cell-matrix adhesion|negative regulation of protein glycosylation in Golgi|positive regulation of cell proliferation|response to retinoic acid|sphingosine biosynthetic process	integral to Golgi membrane	ceramidase activity			haematopoietic_and_lymphoid_tissue(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	20047271	20047274	+	IGR	DEL	TGTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20047271_20047274delTGTT								SLC24A2 (258463 upstream) : MLLT3 (297694 downstream)																																			---	---	---	---
MLLT3	4300	broad.mit.edu	37	9	20448401	20448401	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20448401delA	uc003zoe.2	-						MLLT3_uc011lne.1_Intron|MLLT3_uc011lnf.1_Intron|MLLT3_uc003zof.2_Intron|MLLT3_uc011lng.1_Intron	NM_004529	NP_004520			myeloid/lymphoid or mixed-lineage leukemia						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)				T	MLL	ALL								---	---	---	---
KIAA1797	54914	broad.mit.edu	37	9	20909018	20909018	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20909018delA	uc003zog.1	+						KIAA1797_uc003zoh.1_Intron	NM_017794	NP_060264			hypothetical protein LOC54914							integral to membrane	binding			ovary(8)|breast(1)|kidney(1)	10				GBM - Glioblastoma multiforme(3;2.1e-125)|Lung(42;2.76e-14)|LUSC - Lung squamous cell carcinoma(42;1.99e-11)														---	---	---	---
IFNA14	3448	broad.mit.edu	37	9	21207319	21207319	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21207319delT	uc003zoo.1	-						IFNA10_uc003zoq.1_5'Flank	NM_002172				interferon, alpha 14 precursor						blood coagulation|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	extracellular space	cytokine activity|cytokine receptor binding				0				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	21421939	21421939	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21421939delG								IFNA8 (11755 upstream) : IFNA1 (18501 downstream)																																			---	---	---	---
MTAP	4507	broad.mit.edu	37	9	21946891	21946891	+	Intron	DEL	A	-	-	rs2811718	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21946891delA	uc003zpi.1	+							NM_002451	NP_002442			5'-methylthioadenosine phosphorylase						nucleoside metabolic process	cytoplasm	phosphorylase activity|S-methyl-5-thioadenosine phosphorylase activity			central_nervous_system(1)	1		all_cancers(5;0)|Hepatocellular(5;0.00162)|Colorectal(97;0.173)		GBM - Glioblastoma multiforme(3;0)|Lung(24;2.24e-57)|LUSC - Lung squamous cell carcinoma(38;1.97e-36)|STAD - Stomach adenocarcinoma(4;3.26e-05)|OV - Ovarian serous cystadenocarcinoma(39;0.00931)|COAD - Colon adenocarcinoma(8;0.15)	Adenine(DB00173)													---	---	---	---
Unknown	0	broad.mit.edu	37	9	22383712	22383713	+	IGR	INS	-	C	C	rs2026078	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22383712_22383713insC								CDKN2BAS (262621 upstream) : DMRTA1 (63127 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	22609548	22609548	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22609548delT								DMRTA1 (157076 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	22823496	22823497	+	RNA	INS	-	C	C	rs138867609	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22823496_22823497insC	uc003zpq.1	+	6		c.1631_1632insC								Homo sapiens cDNA FLJ35282 fis, clone PROST2007328.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	22980462	22980462	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22980462delA								DMRTA1 (527990 upstream) : ELAVL2 (709643 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	23083005	23083005	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23083005delT								DMRTA1 (630533 upstream) : ELAVL2 (607100 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	23209384	23209387	+	IGR	DEL	ACAC	-	-	rs111636601		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23209384_23209387delACAC								DMRTA1 (756912 upstream) : ELAVL2 (480718 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	23358916	23358916	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23358916delA								DMRTA1 (906444 upstream) : ELAVL2 (331189 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	25142344	25142347	+	IGR	DEL	ACAC	-	-	rs59606343		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:25142344_25142347delACAC								None (None upstream) : TUSC1 (534047 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	25414787	25414787	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:25414787delA								None (None upstream) : TUSC1 (261607 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	25607865	25607866	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:25607865_25607866delTT								None (None upstream) : TUSC1 (68528 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	26649002	26649002	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26649002delA								TUSC1 (970146 upstream) : C9orf82 (191682 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	26744192	26744192	+	IGR	DEL	A	-	-	rs35284952		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26744192delA								None (None upstream) : C9orf82 (96492 downstream)																																			---	---	---	---
LINGO2	158038	broad.mit.edu	37	9	28469270	28469270	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:28469270delA	uc010mjf.1	-						LINGO2_uc003zqv.1_Intron	NM_152570	NP_689783			leucine rich repeat and Ig domain containing 2							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	Melanoma(11;0.242)	all_neural(11;2.78e-09)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0818)|GBM - Glioblastoma multiforme(2;1.31e-34)|all cancers(2;2.37e-25)|Lung(2;7.48e-08)|LUSC - Lung squamous cell carcinoma(38;5.09e-07)|KIRC - Kidney renal clear cell carcinoma(2;0.0465)|Kidney(2;0.0604)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	29655232	29655233	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:29655232_29655233delTG								MIR873 (766279 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	31711313	31711313	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:31711313delA								None (None upstream) : ACO1 (673288 downstream)																																			---	---	---	---
TOPORS	10210	broad.mit.edu	37	9	32541246	32541246	+	3'UTR	DEL	A	-	-	rs78113455		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32541246delA	uc003zrb.2	-	3					TOPORS_uc003zrc.2_3'UTR	NM_005802	NP_005793			topoisomerase I binding, arginine/serine-rich						DNA damage response, signal transduction resulting in induction of apoptosis|maintenance of protein location in nucleus|proteasomal ubiquitin-dependent protein catabolic process|protein sumoylation|transcription, DNA-dependent	nuclear speck|PML body	antigen binding|DNA binding|DNA topoisomerase I binding|SUMO ligase activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)														---	---	---	---
B4GALT1	2683	broad.mit.edu	37	9	33128095	33128096	+	Intron	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33128095_33128096delCT	uc003zsg.2	-							NM_001497	NP_001488			UDP-Gal:betaGlcNAc beta 1,4-						oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	basolateral plasma membrane|brush border membrane|desmosome|external side of plasma membrane|extracellular region|glycocalyx|Golgi cisterna membrane|Golgi trans cisterna|integral to membrane	alpha-tubulin binding|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity|beta-tubulin binding|lactose synthase activity|metal ion binding|N-acetyllactosamine synthase activity|protein binding|protein homodimerization activity				0			LUSC - Lung squamous cell carcinoma(29;0.0084)	GBM - Glioblastoma multiforme(74;0.121)	N-Acetyl-D-glucosamine(DB00141)													---	---	---	---
B4GALT1	2683	broad.mit.edu	37	9	33129255	33129255	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33129255delT	uc003zsg.2	-							NM_001497	NP_001488			UDP-Gal:betaGlcNAc beta 1,4-						oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	basolateral plasma membrane|brush border membrane|desmosome|external side of plasma membrane|extracellular region|glycocalyx|Golgi cisterna membrane|Golgi trans cisterna|integral to membrane	alpha-tubulin binding|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity|beta-tubulin binding|lactose synthase activity|metal ion binding|N-acetyllactosamine synthase activity|protein binding|protein homodimerization activity				0			LUSC - Lung squamous cell carcinoma(29;0.0084)	GBM - Glioblastoma multiforme(74;0.121)	N-Acetyl-D-glucosamine(DB00141)													---	---	---	---
B4GALT1	2683	broad.mit.edu	37	9	33147257	33147263	+	Intron	DEL	TTTTTTC	-	-	rs142582910		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33147257_33147263delTTTTTTC	uc003zsg.2	-							NM_001497	NP_001488			UDP-Gal:betaGlcNAc beta 1,4-						oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	basolateral plasma membrane|brush border membrane|desmosome|external side of plasma membrane|extracellular region|glycocalyx|Golgi cisterna membrane|Golgi trans cisterna|integral to membrane	alpha-tubulin binding|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity|beta-tubulin binding|lactose synthase activity|metal ion binding|N-acetyllactosamine synthase activity|protein binding|protein homodimerization activity				0			LUSC - Lung squamous cell carcinoma(29;0.0084)	GBM - Glioblastoma multiforme(74;0.121)	N-Acetyl-D-glucosamine(DB00141)													---	---	---	---
B4GALT1	2683	broad.mit.edu	37	9	33166712	33166712	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33166712delG	uc003zsg.2	-							NM_001497	NP_001488			UDP-Gal:betaGlcNAc beta 1,4-						oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	basolateral plasma membrane|brush border membrane|desmosome|external side of plasma membrane|extracellular region|glycocalyx|Golgi cisterna membrane|Golgi trans cisterna|integral to membrane	alpha-tubulin binding|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity|beta-tubulin binding|lactose synthase activity|metal ion binding|N-acetyllactosamine synthase activity|protein binding|protein homodimerization activity				0			LUSC - Lung squamous cell carcinoma(29;0.0084)	GBM - Glioblastoma multiforme(74;0.121)	N-Acetyl-D-glucosamine(DB00141)													---	---	---	---
SUGT1P1	441394	broad.mit.edu	37	9	33227209	33227209	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33227209delT	uc010mjq.1	-							NR_003667				Homo sapiens suppressor of G2 allele of SKP1 pseudogene (S. cerevisiae) (SUGT1P), non-coding RNA.												0																		---	---	---	---
PTENP1	11191	broad.mit.edu	37	9	33675365	33675365	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33675365delA	uc003zth.3	-	1						NR_023917				SubName: Full=Phosphatase and tensin homolog 2; Flags: Fragment;												0																		---	---	---	---
DCAF12	25853	broad.mit.edu	37	9	34099591	34099591	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34099591delT	uc003ztt.2	-							NM_015397	NP_056212			DDB1 and CUL4 associated factor 12							centrosome|CUL4 RING ubiquitin ligase complex					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	34157084	34157084	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34157084delT								DCAF12 (30313 upstream) : UBAP1 (21927 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	34349229	34349229	+	IGR	DEL	C	-	-	rs117323739		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34349229delC								NUDT2 (5534 upstream) : KIAA1161 (19679 downstream)																																			---	---	---	---
KIAA1161	57462	broad.mit.edu	37	9	34370702	34370702	+	3'UTR	DEL	G	-	-	rs72012681		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34370702delG	uc003zue.3	-	3						NM_020702	NP_065753			hypothetical protein LOC57462						carbohydrate metabolic process	integral to membrane	hydrolase activity, hydrolyzing O-glycosyl compounds			ovary(1)|breast(1)|central_nervous_system(1)	3			LUSC - Lung squamous cell carcinoma(29;0.0107)	GBM - Glioblastoma multiforme(74;0.126)														---	---	---	---
C9orf25	203259	broad.mit.edu	37	9	34416309	34416312	+	Intron	DEL	GAAG	-	-	rs10115501		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34416309_34416312delGAAG	uc011lok.1	-						C9orf25_uc003zuj.2_Intron|C9orf25_uc003zuk.2_Intron|C9orf25_uc011lol.1_Intron|C9orf25_uc003zul.2_Intron	NM_147202	NP_671735			hypothetical protein LOC203259												0	all_epithelial(49;0.244)		LUSC - Lung squamous cell carcinoma(29;0.0107)	GBM - Glioblastoma multiforme(74;0.0858)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	34697324	34697324	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34697324delT								CCL19 (6050 upstream) : CCL21 (11680 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	34708322	34708322	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34708322delA								CCL19 (17048 upstream) : CCL21 (682 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	34907747	34907747	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34907747delT								C9orf144 (69164 upstream) : KIAA1045 (49774 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	35007432	35007434	+	IGR	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35007432_35007434delTTT								DNAJB5 (9004 upstream) : C9orf131 (33668 downstream)																																			---	---	---	---
UNC13B	10497	broad.mit.edu	37	9	35161082	35161082	+	5'Flank	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35161082delA	uc003zwq.2	+						UNC13B_uc010mkl.1_5'Flank|UNC13B_uc003zwr.2_5'Flank	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)															---	---	---	---
FAM166B	730112	broad.mit.edu	37	9	35565333	35565334	+	5'Flank	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35565333_35565334insA	uc010mkr.2	-						FAM166B_uc011lov.1_5'Flank|FAM166B_uc011low.1_5'Flank|FAM166B_uc003zwy.2_5'Flank	NM_001164310	NP_001157782			hypothetical protein LOC730112 isoform 1												0																		---	---	---	---
FAM166B	730112	broad.mit.edu	37	9	35565975	35565975	+	5'Flank	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35565975delA	uc010mkr.2	-						FAM166B_uc011lov.1_5'Flank|FAM166B_uc011low.1_5'Flank|FAM166B_uc003zwy.2_5'Flank	NM_001164310	NP_001157782			hypothetical protein LOC730112 isoform 1												0																		---	---	---	---
RECK	8434	broad.mit.edu	37	9	36123173	36123173	+	3'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36123173delT	uc003zyv.2	+	21					RECK_uc003zyw.2_3'UTR|RECK_uc003zyx.2_RNA	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)															---	---	---	---
RNF38	152006	broad.mit.edu	37	9	36353341	36353341	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36353341delA	uc003zzh.2	-						RNF38_uc003zzi.2_Intron|RNF38_uc003zzj.2_Intron|RNF38_uc003zzk.2_Intron|RNF38_uc003zzl.2_Intron|RNF38_uc003zzm.2_Intron	NM_022781	NP_073618			ring finger protein 38 isoform 1								zinc ion binding			central_nervous_system(1)	1			STAD - Stomach adenocarcinoma(86;0.228)															---	---	---	---
MELK	9833	broad.mit.edu	37	9	36671220	36671220	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36671220delT	uc003zzn.2	+						MELK_uc011lpm.1_Intron|MELK_uc011lpn.1_Intron|MELK_uc011lpo.1_Intron|MELK_uc010mll.2_Intron|MELK_uc011lpp.1_Intron|MELK_uc010mlm.2_Intron|MELK_uc011lpq.1_Intron|MELK_uc011lpr.1_Intron|MELK_uc011lps.1_Intron	NM_014791	NP_055606			maternal embryonic leucine zipper kinase							cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	6		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)															---	---	---	---
RG9MTD3	158234	broad.mit.edu	37	9	37768335	37768335	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37768335delA	uc004aai.2	+						RG9MTD3_uc011lqo.1_Intron|RG9MTD3_uc011lqp.1_Intron|RG9MTD3_uc011lqq.1_Intron|RG9MTD3_uc004aaj.2_Intron|RG9MTD3_uc004aak.2_Intron	NM_144964	NP_659401			RNA (guanine-9-) methyltransferase domain								methyltransferase activity				0				GBM - Glioblastoma multiforme(29;0.00817)|Lung(182;0.226)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	38136746	38136747	+	IGR	INS	-	CCCCGGC	CCCCGGC	rs139222324	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38136746_38136747insCCCCGGC								SHB (67536 upstream) : ALDH1B1 (255955 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	38194595	38194595	+	IGR	DEL	A	-	-	rs76037942		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38194595delA								SHB (125385 upstream) : ALDH1B1 (198107 downstream)																																			---	---	---	---
CNTNAP3	79937	broad.mit.edu	37	9	39166200	39166200	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:39166200delA	uc004abi.2	-						CNTNAP3_uc004abj.2_Intron|CNTNAP3_uc011lqr.1_Intron|CNTNAP3_uc004abk.1_Intron|CNTNAP3_uc011lqs.1_Intron|CNTNAP3_uc004abl.1_Intron	NM_033655	NP_387504			cell recognition molecule CASPR3 precursor						cell adhesion|cell recognition|signal transduction	extracellular region|integral to membrane|plasma membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	39817161	39817161	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:39817161delA								LOC653501 (308273 upstream) : FAM74A1 (83039 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	44776750	44776750	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:44776750delT								None (None upstream) : FAM27C (213486 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	46280694	46280719	+	IGR	DEL	TTGCCTGGAGAGAATAACAATCTATA	-	-	rs77092508	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:46280694_46280719delTTGCCTGGAGAGAATAACAATCTATA								FAM27A (552412 upstream) : KGFLP1 (406847 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	46887950	46887951	+	IGR	DEL	GG	-	-	rs111830652	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:46887950_46887951delGG								KGFLP1 (139565 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	66469204	66469204	+	RNA	DEL	G	-	-	rs1047837	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66469204delG	uc004aec.2	+	5		c.2771delG								Homo sapiens, clone IMAGE:5213378, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	66826477	66826477	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66826477delA								LOC442421 (323450 upstream) : AQP7P1 (427790 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	67316293	67316294	+	IGR	INS	-	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67316293_67316294insC								AQP7P1 (26801 upstream) : FAM27B (476636 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	68480277	68480277	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68480277delA								FAM27B (686088 upstream) : MIR1299 (521962 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	69829080	69829080	+	IGR	DEL	A	-	-	rs140553488		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69829080delA								LOC100133920 (164131 upstream) : FOXD4L5 (346629 downstream)																																			---	---	---	---
PIP5K1B	8395	broad.mit.edu	37	9	71459865	71459865	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71459865delA	uc004agu.2	+						PIP5K1B_uc011lrq.1_Intron|PIP5K1B_uc004agv.2_Intron	NM_003558	NP_003549			phosphatidylinositol-4-phosphate 5-kinase, type							endomembrane system|membrane|uropod	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|protein binding			stomach(1)	1				Lung(182;0.133)														---	---	---	---
PIP5K1B	8395	broad.mit.edu	37	9	71619254	71619255	+	Intron	DEL	TG	-	-	rs113022979		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71619254_71619255delTG	uc004agu.2	+						PIP5K1B_uc011lrq.1_Intron|PIP5K1B_uc004agv.2_Intron	NM_003558	NP_003549			phosphatidylinositol-4-phosphate 5-kinase, type							endomembrane system|membrane|uropod	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|protein binding			stomach(1)	1				Lung(182;0.133)														---	---	---	---
TJP2	9414	broad.mit.edu	37	9	71827610	71827610	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71827610delT	uc004ahe.2	+						TJP2_uc011lrs.1_Intron|TJP2_uc004ahb.1_Intron|TJP2_uc011lrt.1_Intron|TJP2_uc004ahd.2_Intron|TJP2_uc004ahf.2_Intron|TJP2_uc011lru.1_Intron|TJP2_uc011lrv.1_Intron	NM_004817	NP_004808			tight junction protein 2 (zona occludens 2)						cellular component disassembly involved in apoptosis	adherens junction|cytoplasm|nucleus|tight junction	guanylate kinase activity|protein binding				0																		---	---	---	---
FAM189A2	9413	broad.mit.edu	37	9	71982212	71982212	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71982212delT	uc010mon.1	+						FAM189A2_uc004ahg.2_Intron	NM_001127608	NP_001121080			chromosome 9 open reading frame 61 precursor							integral to membrane					0																		---	---	---	---
PTAR1	375743	broad.mit.edu	37	9	72365095	72365095	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72365095delA	uc004ahj.3	-						PTAR1_uc004ahi.2_Intron	NM_001099666	NP_001093136			protein prenyltransferase alpha subunit repeat						protein prenylation		protein prenyltransferase activity			central_nervous_system(1)	1																		---	---	---	---
C9orf135	138255	broad.mit.edu	37	9	72499771	72499772	+	Intron	INS	-	T	T	rs140936725	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72499771_72499772insT	uc004ahl.2	+						C9orf135_uc011lrw.1_Intron|C9orf135_uc010moq.2_Intron|C9orf135_uc011lrx.1_Intron|C9orf135_uc010mop.2_Intron	NM_001010940	NP_001010940			hypothetical protein LOC138255							integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	72539516	72539519	+	IGR	DEL	TGTG	-	-	rs147510443		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72539516_72539519delTGTG								C9orf135 (18369 upstream) : MAMDC2 (118978 downstream)																																			---	---	---	---
MAMDC2	256691	broad.mit.edu	37	9	72794268	72794269	+	Intron	INS	-	AC	AC	rs151239823	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72794268_72794269insAC	uc004ahm.2	+						MAMDC2_uc004ahn.2_Intron	NM_153267	NP_694999			MAM domain containing 2 precursor							endoplasmic reticulum|membrane				central_nervous_system(1)|pancreas(1)	2																		---	---	---	---
SMC5	23137	broad.mit.edu	37	9	72895960	72895961	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72895960_72895961delTT	uc004ahr.2	+							NM_015110	NP_055925			SMC5 protein						DNA recombination|DNA repair	chromosome|nucleus	ATP binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
SMC5	23137	broad.mit.edu	37	9	72933303	72933304	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72933303_72933304delAA	uc004ahr.2	+						uc004ahs.1_5'Flank	NM_015110	NP_055925			SMC5 protein						DNA recombination|DNA repair	chromosome|nucleus	ATP binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
KLF9	687	broad.mit.edu	37	9	73005574	73005575	+	Intron	DEL	CT	-	-	rs13299436	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73005574_73005575delCT	uc004aht.2	-							NM_001206	NP_001197			Kruppel-like factor 9						regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
TMC1	117531	broad.mit.edu	37	9	75430881	75430882	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75430881_75430882delAA	uc004aiz.1	+						TMC1_uc010moz.1_Intron|TMC1_uc004aja.1_Intron|TMC1_uc004ajb.1_Intron|TMC1_uc004ajc.1_Intron|TMC1_uc010mpa.1_Intron	NM_138691	NP_619636			transmembrane channel-like 1						sensory perception of sound	integral to membrane				ovary(1)	1																		---	---	---	---
ALDH1A1	216	broad.mit.edu	37	9	75533865	75533865	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75533865delT	uc004ajd.2	-						ALDH1A1_uc011lsh.1_Intron|ALDH1A1_uc011lsg.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)													---	---	---	---
Unknown	0	broad.mit.edu	37	9	75846428	75846428	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75846428delT								ANXA1 (61121 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	76091073	76091073	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:76091073delT								ANXA1 (305766 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	78019137	78019138	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78019137_78019138delTT								OSTF1 (257024 upstream) : PCSK5 (486422 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	78100912	78100912	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78100912delA								OSTF1 (338799 upstream) : PCSK5 (404648 downstream)																																			---	---	---	---
PCSK5	5125	broad.mit.edu	37	9	78794417	78794418	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78794417_78794418delAA	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	78946583	78946583	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78946583delA	uc004akc.1	+											Homo sapiens cDNA FLJ16215 fis, clone CTONG2025610, moderately similar to PC6B.																														---	---	---	---
GCNT1	2650	broad.mit.edu	37	9	79054697	79054697	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79054697delC	uc010mpf.2	+						GCNT1_uc010mpg.2_5'Flank	NM_001490	NP_001481			beta-1,3-galactosyl-O-glycosyl-glycoprotein						protein O-linked glycosylation	Golgi membrane|integral to membrane	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	79211456	79211456	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79211456delA								GCNT1 (89126 upstream) : PRUNE2 (14837 downstream)																																			---	---	---	---
PRUNE2	158471	broad.mit.edu	37	9	79340480	79340480	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79340480delA	uc010mpk.2	-							NM_015225	NP_056040			prune homolog 2						apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0																		---	---	---	---
PRUNE2	158471	broad.mit.edu	37	9	79436465	79436465	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79436465delT	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	79757008	79757008	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79757008delT								FOXB2 (121139 upstream) : VPS13A (35353 downstream)																																			---	---	---	---
VPS13A	23230	broad.mit.edu	37	9	79898258	79898258	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79898258delT	uc004akr.2	+						VPS13A_uc004akp.3_Intron|VPS13A_uc004akq.3_Intron|VPS13A_uc004aks.2_Intron	NM_033305	NP_150648			vacuolar protein sorting 13A isoform A						Golgi to endosome transport|protein transport	intracellular	protein binding			pancreas(3)|skin(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	10																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	81230914	81230914	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81230914delA								PSAT1 (285907 upstream) : TLE4 (955964 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	82158514	82158514	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82158514delT								None (None upstream) : TLE4 (28364 downstream)																																			---	---	---	---
TLE4	7091	broad.mit.edu	37	9	82190764	82190765	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82190764_82190765insT	uc004ald.2	+						TLE4_uc004alc.2_Intron|TLE4_uc010mpr.2_Intron|TLE4_uc004ale.2_Intron|TLE4_uc011lsq.1_Intron|TLE4_uc010mps.2_Intron|TLE4_uc004alf.2_Intron	NM_007005	NP_008936			transducin-like enhancer protein 4											lung(2)|ovary(1)|breast(1)|skin(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	82379668	82379668	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82379668delA								TLE4 (38011 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	83653236	83653236	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:83653236delT								None (None upstream) : TLE1 (545364 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	84759957	84759957	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84759957delT								FLJ46321 (149787 upstream) : RASEF (837360 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	85213141	85213142	+	IGR	DEL	TG	-	-	rs72042271		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85213141_85213142delTG								FLJ46321 (602971 upstream) : RASEF (384175 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	85239287	85239287	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85239287delA								FLJ46321 (629117 upstream) : RASEF (358030 downstream)																																			---	---	---	---
HNRNPK	3190	broad.mit.edu	37	9	86584095	86584096	+	3'UTR	INS	-	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86584095_86584096insC	uc004ang.3	-	17					HNRNPK_uc011lsw.1_3'UTR|HNRNPK_uc004and.3_3'UTR|HNRNPK_uc004ank.3_3'UTR|HNRNPK_uc004anf.3_3'UTR|HNRNPK_uc004anh.3_3'UTR|HNRNPK_uc011lsx.1_3'UTR|HNRNPK_uc004ani.3_3'UTR|HNRNPK_uc004anj.3_3'UTR|HNRNPK_uc004ann.3_3'UTR|HNRNPK_uc004anl.3_3'UTR|HNRNPK_uc004anm.3_3'UTR	NM_031262	NP_112552			heterogeneous nuclear ribonucleoprotein K						interspecies interaction between organisms|positive regulation of low-density lipoprotein particle receptor biosynthetic process|positive regulation of receptor-mediated endocytosis|regulation of lipid transport by positive regulation of transcription from an RNA polymerase II promoter|regulation of low-density lipoprotein particle clearance|signal transduction	catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nuclear chromatin|nucleoplasm	protein binding|RNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|single-stranded DNA binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	86693417	86693417	+	Intron	DEL	A	-	-	rs34077830		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86693417delA	uc004ant.2	+											Homo sapiens mRNA; cDNA DKFZp779O1559 (from clone DKFZp779O1559).																														---	---	---	---
SLC28A3	64078	broad.mit.edu	37	9	86895090	86895090	+	Intron	DEL	T	-	-	rs35540005		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86895090delT	uc010mpz.2	-						SLC28A3_uc011lsy.1_Intron|SLC28A3_uc004anu.1_Intron	NM_022127	NP_071410			concentrative Na+-nucleoside cotransporter						nucleobase, nucleoside and nucleotide metabolic process	integral to membrane|plasma membrane	nucleoside binding			upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	87100005	87100005	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87100005delA								SLC28A3 (116592 upstream) : NTRK2 (183461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	87221108	87221110	+	IGR	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87221108_87221110delAAA								SLC28A3 (237695 upstream) : NTRK2 (62356 downstream)																																			---	---	---	---
NTRK2	4915	broad.mit.edu	37	9	87559106	87559106	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87559106delG	uc004aoa.1	+						NTRK2_uc004any.1_Intron|NTRK2_uc004anz.1_Intron	NM_001018064	NP_001018074			neurotrophic tyrosine kinase, receptor, type 2						activation of adenylate cyclase activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development	integral to plasma membrane	ATP binding|neurotrophin receptor activity|transmembrane receptor protein tyrosine kinase activity			lung(11)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|liver(1)	16															TSP Lung(25;0.17)			---	---	---	---
Unknown	0	broad.mit.edu	37	9	87729195	87729196	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87729195_87729196delTC								NTRK2 (90690 upstream) : AGTPBP1 (432259 downstream)																																			---	---	---	---
AGTPBP1	23287	broad.mit.edu	37	9	88327180	88327180	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88327180delA	uc011ltd.1	-						AGTPBP1_uc010mqc.2_Intron|AGTPBP1_uc011lte.1_Intron	NM_015239	NP_056054			ATP/GTP binding protein 1						C-terminal protein deglutamylation|cerebellar Purkinje cell differentiation|eye photoreceptor cell differentiation|mitochondrion organization|neuromuscular process|olfactory bulb development|protein side chain deglutamylation|proteolysis	cytosol|mitochondrion|nucleus	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(4)|large_intestine(2)|skin(1)	7																		---	---	---	---
AGTPBP1	23287	broad.mit.edu	37	9	88330161	88330161	+	5'Flank	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88330161delA	uc011ltd.1	-						AGTPBP1_uc010mqc.2_Intron|AGTPBP1_uc011lte.1_Intron	NM_015239	NP_056054			ATP/GTP binding protein 1						C-terminal protein deglutamylation|cerebellar Purkinje cell differentiation|eye photoreceptor cell differentiation|mitochondrion organization|neuromuscular process|olfactory bulb development|protein side chain deglutamylation|proteolysis	cytosol|mitochondrion|nucleus	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(4)|large_intestine(2)|skin(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	88524199	88524200	+	IGR	DEL	AA	-	-	rs79951575		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88524199_88524200delAA								AGTPBP1 (167255 upstream) : NAA35 (31857 downstream)																																			---	---	---	---
NAA35	60560	broad.mit.edu	37	9	88571356	88571356	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88571356delT	uc004aoi.3	+						NAA35_uc004aoj.3_Intron|NAA35_uc004aok.1_Intron	NM_024635	NP_078911			corneal wound healing-related protein						smooth muscle cell proliferation	cytoplasm|nucleus|plasma membrane				skin(2)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	89176366	89176367	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89176366_89176367delTT								ZCCHC6 (206988 upstream) : GAS1 (382912 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	89450669	89450669	+	IGR	DEL	A	-	-	rs79189061	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89450669delA								ZCCHC6 (481291 upstream) : GAS1 (108610 downstream)																																			---	---	---	---
DAPK1	1612	broad.mit.edu	37	9	90317794	90317794	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90317794delA	uc004apc.2	+						DAPK1_uc004apd.2_Intron|DAPK1_uc011ltg.1_Intron|DAPK1_uc011lth.1_Intron	NM_004938	NP_004929			death-associated protein kinase 1						apoptosis|induction of apoptosis by extracellular signals|intracellular protein kinase cascade	actin cytoskeleton|cytoplasm	ATP binding|calmodulin binding|protein serine/threonine kinase activity			ovary(1)|breast(1)	2														Chronic_Lymphocytic_Leukemia_Familial_Clustering_of				---	---	---	---
C9orf79	286234	broad.mit.edu	37	9	90500227	90500227	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90500227delC	uc004app.3	+	4	860	c.825delC	c.(823-825)GTCfs	p.V275fs	C9orf79_uc004apo.1_Frame_Shift_Del_p.V87fs	NM_178828	NP_849150	Q6ZUB1	CI079_HUMAN	chromosome 9 open reading frame 79	275	Pro-rich.					integral to membrane				ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	90763176	90763176	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90763176delA								CDK20 (173509 upstream) : SPIN1 (239664 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	90937881	90937881	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90937881delA								CDK20 (348214 upstream) : SPIN1 (64959 downstream)																																			---	---	---	---
SPIN1	10927	broad.mit.edu	37	9	91057327	91057329	+	Intron	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91057327_91057329delTTT	uc010mqj.2	+						SPIN1_uc004apy.2_Intron|SPIN1_uc004apz.2_Intron|SPIN1_uc010mqk.2_Intron	NM_006717	NP_006708			spindlin						cell cycle|gamete generation|multicellular organismal development	nucleus	methylated histone residue binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	91345096	91345096	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91345096delA								LOC286238 (78021 upstream) : C9orf47 (260682 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	91601734	91601736	+	IGR	DEL	TAA	-	-	rs150766267		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91601734_91601736delTAA								LOC286238 (334659 upstream) : C9orf47 (4042 downstream)																																			---	---	---	---
SHC3	53358	broad.mit.edu	37	9	91633405	91633405	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91633405delA	uc004aqg.2	-							NM_016848	NP_058544			src homology 2 domain-containing transforming						central nervous system development|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol	protein binding|signal transducer activity			lung(3)|skin(1)	4																		---	---	---	---
SHC3	53358	broad.mit.edu	37	9	91684351	91684351	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91684351delA	uc004aqg.2	-							NM_016848	NP_058544			src homology 2 domain-containing transforming						central nervous system development|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol	protein binding|signal transducer activity			lung(3)|skin(1)	4																		---	---	---	---
SHC3	53358	broad.mit.edu	37	9	91723456	91723457	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91723456_91723457delAC	uc004aqg.2	-							NM_016848	NP_058544			src homology 2 domain-containing transforming						central nervous system development|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol	protein binding|signal transducer activity			lung(3)|skin(1)	4																		---	---	---	---
SEMA4D	10507	broad.mit.edu	37	9	91978183	91978183	+	Intron	DEL	C	-	-	rs67247190		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91978183delC	uc011ltm.1	-						SEMA4D_uc011ltn.1_Intron|SEMA4D_uc011lto.1_Intron|SEMA4D_uc004aql.2_Intron|SEMA4D_uc004aqm.2_Intron	NM_001142287	NP_001135759			semaphorin 4D isoform 2						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	94169166	94169166	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94169166delA								AUH (44960 upstream) : NFIL3 (2163 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	94227926	94227926	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94227926delT								NFIL3 (41782 upstream) : ROR2 (97447 downstream)																																			---	---	---	---
ROR2	4920	broad.mit.edu	37	9	94656266	94656266	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94656266delT	uc004arj.1	-						ROR2_uc004ari.1_Intron|ROR2_uc004ark.2_Intron	NM_004560	NP_004551			receptor tyrosine kinase-like orphan receptor 2						negative regulation of cell proliferation|positive regulation of cell migration|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			lung(8)|central_nervous_system(5)|ovary(3)|large_intestine(2)|stomach(1)|breast(1)	20																		---	---	---	---
NOL8	55035	broad.mit.edu	37	9	95085870	95085870	+	Intron	DEL	A	-	-	rs75489638		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95085870delA	uc004arv.2	-						CENPP_uc004arz.2_5'Flank|CENPP_uc010mqx.2_5'Flank|NOL8_uc004arw.2_Intron|NOL8_uc011ltw.1_Intron|NOL8_uc004arx.2_Intron|CENPP_uc004ary.1_5'Flank	NM_017948	NP_060418			nucleolar protein 8						DNA replication|positive regulation of cell growth	nucleolus	nucleotide binding|protein binding|RNA binding			ovary(1)	1																		---	---	---	---
CENPP	401541	broad.mit.edu	37	9	95127858	95127858	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95127858delA	uc004arz.2	+						CENPP_uc010mqx.2_Intron|CENPP_uc004ary.1_Intron	NM_001012267	NP_001012267			centromere protein P						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	chromosome, centromeric region|cytosol|nucleoplasm				ovary(2)	2																		---	---	---	---
ECM2	1842	broad.mit.edu	37	9	95290912	95290912	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95290912delA	uc004ash.2	-						CENPP_uc004arz.2_Intron|CENPP_uc010mqx.2_Intron|ECM2_uc004asf.3_Intron|ECM2_uc011lty.1_Intron|ECM2_uc004asg.2_Intron|ECM2_uc011ltz.1_Intron	NM_001393	NP_001384			extracellular matrix protein 2 precursor						cell-matrix adhesion		integrin binding			ovary(1)|skin(1)	2																		---	---	---	---
WNK2	65268	broad.mit.edu	37	9	96056224	96056225	+	Intron	INS	-	TC	TC	rs62571758		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96056224_96056225insTC	uc004ati.1	+						WNK2_uc011lud.1_Intron|WNK2_uc004atj.2_Intron|WNK2_uc004atk.2_Intron|WNK2_uc004atl.1_Intron	NM_006648	NP_006639			WNK lysine deficient protein kinase 2						intracellular protein kinase cascade		ATP binding|protein binding|protein serine/threonine kinase activity			lung(4)|stomach(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)|breast(1)	12																		---	---	---	---
FAM120A	23196	broad.mit.edu	37	9	96236458	96236460	+	Intron	DEL	TTG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96236458_96236460delTTG	uc004atw.2	+						FAM120A_uc004atv.2_Intron|FAM120A_uc004atx.2_Intron|FAM120A_uc004aty.2_Intron	NM_014612	NP_055427			oxidative stress-associated Src activator							cytoplasm|plasma membrane	RNA binding				0																		---	---	---	---
PHF2	5253	broad.mit.edu	37	9	96422612	96422612	+	Frame_Shift_Del	DEL	A	-	-	rs76832193		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96422612delA	uc004aub.2	+	12	1615	c.1468delA	c.(1468-1470)AAAfs	p.K490fs	PHF2_uc011lug.1_Frame_Shift_Del_p.K373fs|PHF2_uc004auc.2_5'Flank	NM_005392	NP_005383	O75151	PHF2_HUMAN	PHD finger protein 2	490	Pro-rich.|Lys-rich.				liver development|negative regulation of chromatin silencing at rDNA|transcription, DNA-dependent	nucleolus	histone demethylase activity (H3-K9 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	96658777	96658777	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96658777delC								PHF2 (216910 upstream) : BARX1 (55134 downstream)																																			---	---	---	---
BARX1	56033	broad.mit.edu	37	9	96714426	96714426	+	3'UTR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96714426delC	uc010mrh.2	-	4					BARX1_uc004aud.2_3'UTR	NM_021570	NP_067545			BARX homeobox 1							nuclear chromosome	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
C9orf3	84909	broad.mit.edu	37	9	97684916	97684917	+	Intron	DEL	TT	-	-	rs113040711		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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)														---	---	---	---
C9orf102	375748	broad.mit.edu	37	9	98693745	98693746	+	Intron	INS	-	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98693745_98693746insC	uc004avt.3	+						C9orf102_uc010mrx.1_Intron|C9orf102_uc011lum.1_Intron|C9orf102_uc010mry.1_Intron|C9orf102_uc010mrz.2_Intron|C9orf102_uc004avu.2_Intron	NM_001010895	NP_001010895			RAD26L hypothetical protein						DNA repair	nucleus	ATP binding|ATP-dependent helicase activity|DNA binding				0		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	98957960	98957960	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98957960delT								NCRNA00092 (173923 upstream) : HSD17B3 (39629 downstream)																																			---	---	---	---
ZNF367	195828	broad.mit.edu	37	9	99165258	99165259	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99165258_99165259delTT	uc004awf.2	-						ZNF367_uc004awg.2_Intron	NM_153695	NP_710162			zinc finger protein 367						regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Acute lymphoblastic leukemia(62;0.0167)																---	---	---	---
HABP4	22927	broad.mit.edu	37	9	99246224	99246224	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99246224delA	uc010msg.2	+						HABP4_uc010msh.2_Intron	NM_014282	NP_055097			hyaluronan binding protein 4						platelet activation|platelet degranulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|extracellular region|nucleus	protein binding			ovary(1)	1		Acute lymphoblastic leukemia(62;0.0169)|all_hematologic(171;0.214)																---	---	---	---
CDC14B	8555	broad.mit.edu	37	9	99308719	99308719	+	Intron	DEL	T	-	-	rs111518660		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99308719delT	uc004awj.2	-						CDC14B_uc004awk.2_Intron|CDC14B_uc004awl.2_Intron|CDC14B_uc004awi.2_Intron	NM_033331	NP_201588			CDC14 homolog B isoform 2						activation of anaphase-promoting complex activity|DNA repair|G2/M transition DNA damage checkpoint	nucleolus|nucleoplasm	protein binding|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(1)	1		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
KIAA1529	57653	broad.mit.edu	37	9	100137284	100137284	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100137284delC	uc011lut.1	+						KIAA1529_uc004axe.1_Intron|KIAA1529_uc004axg.1_Intron|KIAA1529_uc004axh.1_Intron|KIAA1529_uc011luw.1_Intron	NM_020893	NP_065944			hypothetical protein LOC57653											ovary(4)|large_intestine(2)|skin(1)	7		Acute lymphoblastic leukemia(62;0.154)																---	---	---	---
NANS	54187	broad.mit.edu	37	9	100825993	100825993	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100825993delA	uc004ayb.2	+						NANS_uc004ayc.2_Intron	NM_018946	NP_061819			N-acetylneuraminic acid phosphate synthase						lipopolysaccharide biosynthetic process	cytoplasm	N-acetylneuraminate synthase activity|N-acylneuraminate cytidylyltransferase activity|N-acylneuraminate-9-phosphate synthase activity			skin(1)	1		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
CORO2A	7464	broad.mit.edu	37	9	100887458	100887458	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100887458delG	uc004ayl.2	-						CORO2A_uc004aym.2_Intron|CORO2A_uc004ayk.2_Intron	NM_003389	NP_003380			coronin, actin binding protein, 2A						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)																---	---	---	---
CORO2A	7464	broad.mit.edu	37	9	100927222	100927223	+	Intron	INS	-	ACT	ACT	rs149983174	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100927222_100927223insACT	uc004ayl.2	-						CORO2A_uc004aym.2_Intron|CORO2A_uc004ayn.2_Intron	NM_003389	NP_003380			coronin, actin binding protein, 2A						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)																---	---	---	---
GABBR2	9568	broad.mit.edu	37	9	101067559	101067559	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101067559delT	uc004ays.2	-							NM_005458	NP_005449			G protein-coupled receptor 51 precursor						negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(2)|skin(2)	4		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)													---	---	---	---
GABBR2	9568	broad.mit.edu	37	9	101373290	101373291	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101373290_101373291insA	uc004ays.2	-							NM_005458	NP_005449			G protein-coupled receptor 51 precursor						negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(2)|skin(2)	4		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)													---	---	---	---
Unknown	0	broad.mit.edu	37	9	101638476	101638477	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101638476_101638477insA								GALNT12 (26118 upstream) : COL15A1 (67661 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	101652773	101652775	+	IGR	DEL	AGC	-	-	rs75742246		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101652773_101652775delAGC								GALNT12 (40415 upstream) : COL15A1 (53363 downstream)																																			---	---	---	---
COL15A1	1306	broad.mit.edu	37	9	101749335	101749336	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101749335_101749336insA	uc004azb.1	+							NM_001855	NP_001846			alpha 1 type XV collagen precursor						angiogenesis|cell differentiation|signal transduction	collagen type XV|extracellular space|integral to membrane	binding			ovary(6)	6		Acute lymphoblastic leukemia(62;0.0562)																---	---	---	---
TGFBR1	7046	broad.mit.edu	37	9	101894324	101894324	+	Intron	DEL	T	-	-	rs149629526	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101894324delT	uc004azc.2	+						TGFBR1_uc004azd.2_Intron|TGFBR1_uc011lvc.1_Intron|TGFBR1_uc004aze.2_Intron	NM_004612	NP_004603			transforming growth factor, beta receptor I						activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway		ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding			lung(2)|ovary(1)	3		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	102267031	102267032	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102267031_102267032delAA								SEC61B (274131 upstream) : NR4A3 (317105 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	102501197	102501198	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102501197_102501198insA	uc004bad.1	-											Homo sapiens cDNA FLJ32889 fis, clone TESTI2004560.																														---	---	---	---
STX17	55014	broad.mit.edu	37	9	102729626	102729626	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102729626delT	uc004bal.3	+						STX17_uc010msx.2_Intron|STX17_uc011lvd.1_Intron	NM_017919	NP_060389			syntaxin 17						intracellular protein transport|vesicle-mediated transport	endoplasmic reticulum|integral to membrane|nucleolus	SNAP receptor activity			large_intestine(1)	1		Acute lymphoblastic leukemia(62;0.0559)|all_hematologic(171;0.189)																---	---	---	---
INVS	27130	broad.mit.edu	37	9	102868606	102868606	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102868606delT	uc004bap.1	+						INVS_uc010mta.1_Intron|INVS_uc011lve.1_Intron|INVS_uc004bao.1_Intron|INVS_uc004baq.1_Intron|INVS_uc004bar.1_Intron|INVS_uc010mtb.1_Intron	NM_014425	NP_055240			inversin isoform a						negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasm|membrane|microtubule|nucleus|spindle	calmodulin binding			ovary(2)	2		Acute lymphoblastic leukemia(62;0.056)																---	---	---	---
TEX10	54881	broad.mit.edu	37	9	103066284	103066285	+	Intron	DEL	CA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103066284_103066285delCA	uc004bas.2	-						TEX10_uc011lvf.1_Intron|TEX10_uc011lvg.1_Intron	NM_017746	NP_060216			testis expressed 10 isoform 1							integral to membrane|MLL1 complex|nuclear membrane|nucleolus	binding			ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(62;0.0527)		OV - Ovarian serous cystadenocarcinoma(323;0.157)														---	---	---	---
TMEFF1	8577	broad.mit.edu	37	9	103264647	103264647	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103264647delT	uc004baz.1	+						TMEFF1_uc004bay.1_Intron	NM_003692	NP_003683			transmembrane protein with EGF-like and two						multicellular organismal development	integral to membrane|plasma membrane					0		Acute lymphoblastic leukemia(62;0.0452)																---	---	---	---
GRIN3A	116443	broad.mit.edu	37	9	104463405	104463405	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104463405delT	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	104995814	104995814	+	IGR	DEL	A	-	-	rs76616303		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104995814delA								GRIN3A (494952 upstream) : CYLC2 (761779 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	105138175	105138176	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105138175_105138176delTC								GRIN3A (637313 upstream) : CYLC2 (619417 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	105502899	105502900	+	IGR	INS	-	GT	GT	rs149837243	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105502899_105502900insGT								None (None upstream) : CYLC2 (254693 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	105532184	105532184	+	IGR	DEL	T	-	-	rs72283639		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105532184delT								None (None upstream) : CYLC2 (225409 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	105728479	105728479	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105728479delT								None (None upstream) : CYLC2 (29114 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	106396372	106396377	+	IGR	DEL	CACACA	-	-	rs72006970		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106396372_106396377delCACACA								CYLC2 (615602 upstream) : SMC2 (460164 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	107068103	107068103	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107068103delA								SMC2 (164410 upstream) : OR13F1 (198441 downstream)																																			---	---	---	---
ABCA1	19	broad.mit.edu	37	9	107592971	107592971	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107592971delA	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	108781689	108781689	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108781689delA								TMEM38B (244245 upstream) : ZNF462 (843689 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	108815220	108815221	+	IGR	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108815220_108815221delAG								TMEM38B (277776 upstream) : ZNF462 (810157 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	109279779	109279780	+	Intron	DEL	CA	-	-	rs111701084		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109279779_109279780delCA	uc004bcx.2	+											Homo sapiens, clone IMAGE:4246712, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	109293971	109293972	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109293971_109293972insT	uc004bcx.2	+											Homo sapiens, clone IMAGE:4246712, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	109600534	109600535	+	IGR	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109600534_109600535delGT								None (None upstream) : ZNF462 (24843 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	109840072	109840073	+	Intron	INS	-	GT	GT	rs142213929	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109840072_109840073insGT	uc004bdc.1	-											Homo sapiens cDNA FLJ40387 fis, clone TESTI2036129.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	110605453	110605453	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110605453delT								KLF4 (353406 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110700592	110700592	+	IGR	DEL	A	-	-	rs34830525		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110700592delA								KLF4 (448545 upstream) : ACTL7B (916279 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	111890649	111890649	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111890649delA								C9orf5 (8424 upstream) : C9orf4 (8932 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	112091226	112091226	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112091226delA								EPB41L4B (8205 upstream) : PTPN3 (46748 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	112369480	112369480	+	IGR	DEL	C	-	-	rs71495114		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112369480delC								PTPN3 (108887 upstream) : PALM2 (33592 downstream)																																			---	---	---	---
PALM2-AKAP2	445815	broad.mit.edu	37	9	112845597	112845598	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112845597_112845598insT	uc004bei.2	+						PALM2-AKAP2_uc004bek.3_Intron|PALM2-AKAP2_uc004bej.3_Intron|PALM2-AKAP2_uc004bel.1_Intron|AKAP2_uc011lwi.1_Intron|AKAP2_uc004bem.2_Intron	NM_001136562	NP_001130034			A kinase (PRKA) anchor protein 2 isoform 2								enzyme binding			ovary(3)|central_nervous_system(2)|skin(1)	6																		---	---	---	---
LPAR1	1902	broad.mit.edu	37	9	113683874	113683874	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113683874delA	uc004bfa.2	-						LPAR1_uc011lwm.1_Intron|LPAR1_uc004bfb.2_Intron|LPAR1_uc004bfc.2_Intron|LPAR1_uc011lwn.1_Intron|LPAR1_uc011lwo.1_Intron|LPAR1_uc010mub.2_Intron	NM_057159	NP_476500			lysophosphatidic acid receptor 1						positive regulation of I-kappaB kinase/NF-kappaB cascade	cell surface|integral to plasma membrane				ovary(2)	2																		---	---	---	---
UGCG	7357	broad.mit.edu	37	9	114694304	114694304	+	Intron	DEL	A	-	-	rs34569956		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114694304delA	uc004bft.2	+							NM_003358	NP_003349			ceramide glucosyltransferase						epidermis development|glucosylceramide biosynthetic process	Golgi membrane|integral to membrane|membrane fraction	ceramide glucosyltransferase activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(323;0.0433)	Miglustat(DB00419)													---	---	---	---
KIAA1958	158405	broad.mit.edu	37	9	115250227	115250230	+	Intron	DEL	GTGT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115250227_115250230delGTGT	uc004bgf.1	+						KIAA1958_uc011lwx.1_Intron|uc004bge.1_5'Flank	NM_133465	NP_597722			hypothetical protein LOC158405											skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	116473932	116473932	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116473932delA								RGS3 (113915 upstream) : ZNF618 (164630 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	116500350	116500351	+	IGR	INS	-	CTT	CTT	rs10646424		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116500350_116500351insCTT								RGS3 (140333 upstream) : ZNF618 (138211 downstream)																																			---	---	---	---
DFNB31	25861	broad.mit.edu	37	9	117244964	117244965	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117244964_117244965delAA	uc004biz.3	-						DFNB31_uc004biy.3_Intron|DFNB31_uc004bja.3_Intron|DFNB31_uc004bjb.2_Intron	NM_015404	NP_056219			CASK-interacting protein CIP98 isoform 1						inner ear receptor stereocilium organization|retina homeostasis|sensory perception of light stimulus|sensory perception of sound	cytoplasm|growth cone|stereocilium				ovary(4)|central_nervous_system(1)|pancreas(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	118842426	118842426	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118842426delT								C9orf27 (155049 upstream) : PAPPA (73645 downstream)																																			---	---	---	---
ASTN2	23245	broad.mit.edu	37	9	119545500	119545501	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119545500_119545501delTT	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron	NM_198187	NP_937830			astrotactin 2 isoform c							integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9																		---	---	---	---
ASTN2	23245	broad.mit.edu	37	9	119594819	119594819	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119594819delT	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron	NM_198187	NP_937830			astrotactin 2 isoform c							integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9																		---	---	---	---
ASTN2	23245	broad.mit.edu	37	9	119739692	119739693	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119739692_119739693insT	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	120207842	120207842	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120207842delT								ASTN2 (30525 upstream) : TLR4 (258618 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	121544633	121544633	+	IGR	DEL	A	-	-	rs80004143		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:121544633delA								None (None upstream) : DBC1 (384275 downstream)																																			---	---	---	---
DBC1	1620	broad.mit.edu	37	9	122113728	122113728	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122113728delA	uc004bkc.2	-						DBC1_uc004bkd.2_Intron	NM_014618	NP_055433			deleted in bladder cancer 1 precursor						cell cycle arrest|cell death	cytoplasm	protein binding			skin(3)|ovary(2)|central_nervous_system(2)|large_intestine(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	122670856	122670857	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122670856_122670857delTT								DBC1 (539117 upstream) : MIR147 (336400 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	122798503	122798503	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122798503delA								DBC1 (666764 upstream) : MIR147 (208754 downstream)																																			---	---	---	---
FBXW2	26190	broad.mit.edu	37	9	123540601	123540602	+	Intron	INS	-	A	A	rs113452728		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123540601_123540602insA	uc004bkl.1	-						FBXW2_uc011lyc.1_Intron|FBXW2_uc004bkn.2_Intron|FBXW2_uc004bkm.1_Intron|FBXW2_uc010mvj.1_Intron	NM_012164	NP_036296			F-box and WD repeat domain containing 2						proteolysis		protein binding|ubiquitin-protein ligase activity			urinary_tract(1)|ovary(1)|pancreas(1)|skin(1)	4																		---	---	---	---
RABGAP1	23637	broad.mit.edu	37	9	125791597	125791598	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125791597_125791598delTT	uc011lzh.1	+						RABGAP1_uc004bnl.3_Intron	NM_012197	NP_036329			RAB GTPase activating protein 1						cell cycle	centrosome|cytosol|microtubule associated complex	Rab GTPase activator activity|tubulin binding			ovary(3)|kidney(2)	5																		---	---	---	---
DENND1A	57706	broad.mit.edu	37	9	126338787	126338787	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126338787delT	uc004bnz.1	-						DENND1A_uc011lzl.1_Intron|DENND1A_uc004bny.1_Intron|DENND1A_uc011lzm.1_Intron|DENND1A_uc004boa.1_Intron|DENND1A_uc004bob.1_Intron|DENND1A_uc004boc.2_Intron	NM_020946	NP_065997			DENN/MADD domain containing 1A isoform 1							cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2																		---	---	---	---
NR6A1	2649	broad.mit.edu	37	9	127421566	127421566	+	Intron	DEL	G	-	-	rs10986390		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127421566delG	uc004bor.1	-						NR6A1_uc004boq.1_Intron|NR6A1_uc010mwq.1_Intron|uc004bos.2_RNA	NM_033334	NP_201591			nuclear receptor subfamily 6, group A, member 1						cell proliferation|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|spermatogenesis	transcription factor complex	protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(3)	3																		---	---	---	---
NR6A1	2649	broad.mit.edu	37	9	127492265	127492265	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127492265delT	uc004bor.1	-						NR6A1_uc004boq.1_Intron|NR6A1_uc010mwq.1_Intron	NM_033334	NP_201591			nuclear receptor subfamily 6, group A, member 1						cell proliferation|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|spermatogenesis	transcription factor complex	protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(3)	3																		---	---	---	---
OLFML2A	169611	broad.mit.edu	37	9	127549000	127549000	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127549000delA	uc004bov.2	+						OLFML2A_uc010mwr.1_Intron	NM_182487	NP_872293			olfactomedin-like 2A precursor												0																		---	---	---	---
GAPVD1	26130	broad.mit.edu	37	9	128036634	128036634	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128036634delA	uc010mwx.2	+						GAPVD1_uc004bpo.2_Intron|GAPVD1_uc011lzs.1_Intron|GAPVD1_uc004bpp.2_Intron|GAPVD1_uc004bpq.2_Intron	NM_015635	NP_056450			GTPase activating protein and VPS9 domains 1						endocytosis|regulation of protein transport|regulation of small GTPase mediated signal transduction|signal transduction	cytosol|endosome|membrane	GTPase activating protein binding|GTPase activator activity|guanyl-nucleotide exchange factor activity			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
GAPVD1	26130	broad.mit.edu	37	9	128048755	128048756	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128048755_128048756delTT	uc010mwx.2	+						GAPVD1_uc004bpo.2_Intron|GAPVD1_uc011lzs.1_Intron|GAPVD1_uc004bpp.2_Intron|GAPVD1_uc004bpq.2_Intron	NM_015635	NP_056450			GTPase activating protein and VPS9 domains 1						endocytosis|regulation of protein transport|regulation of small GTPase mediated signal transduction|signal transduction	cytosol|endosome|membrane	GTPase activating protein binding|GTPase activator activity|guanyl-nucleotide exchange factor activity			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
MAPKAP1	79109	broad.mit.edu	37	9	128201010	128201010	+	3'UTR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128201010delC	uc004bpv.2	-	12					MAPKAP1_uc011lzt.1_3'UTR|MAPKAP1_uc010mwz.2_RNA|MAPKAP1_uc011lzu.1_3'UTR|MAPKAP1_uc011lzv.1_3'UTR|MAPKAP1_uc004bpw.2_3'UTR|MAPKAP1_uc004bpx.2_3'UTR|MAPKAP1_uc004bpy.2_3'UTR|MAPKAP1_uc004bpz.2_3'UTR|MAPKAP1_uc010mxa.2_RNA|MAPKAP1_uc004bpu.2_RNA	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	128270452	128270452	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128270452delA	uc004bpv.2	-						MAPKAP1_uc011lzt.1_Intron|MAPKAP1_uc010mwz.2_Intron|MAPKAP1_uc011lzu.1_Intron|MAPKAP1_uc011lzv.1_Intron|MAPKAP1_uc004bpw.2_Intron|MAPKAP1_uc004bpx.2_Intron|MAPKAP1_uc004bpy.2_Intron|MAPKAP1_uc004bpz.2_Intron|MAPKAP1_uc010mxa.2_Intron|MAPKAP1_uc010mxb.1_Intron	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	128385075	128385081	+	Intron	DEL	CTCTCCC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128385075_128385081delCTCTCCC	uc004bpv.2	-						MAPKAP1_uc011lzu.1_Intron|MAPKAP1_uc011lzv.1_Intron|MAPKAP1_uc004bpw.2_Intron|MAPKAP1_uc004bpx.2_Intron|MAPKAP1_uc004bpy.2_Intron|MAPKAP1_uc004bpz.2_Intron|MAPKAP1_uc010mxa.2_Intron|MAPKAP1_uc010mxb.1_Intron|MAPKAP1_uc004bqa.2_Intron|MAPKAP1_uc010mxc.1_Intron	NM_001006617	NP_001006618			mitogen-activated protein kinase associated						nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|response to stress|T cell costimulation	cytoplasmic membrane-bounded vesicle|cytosol|nucleus|plasma membrane	Ras GTPase binding			ovary(2)|lung(2)	4																		---	---	---	---
FAM125B	89853	broad.mit.edu	37	9	129208427	129208427	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129208427delT	uc004bqh.1	+						FAM125B_uc011lzy.1_Intron|FAM125B_uc010mxd.2_Intron	NM_033446	NP_258257			hypothetical protein LOC89853 isoform 1						protein transport	late endosome membrane					0																		---	---	---	---
ZBTB43	23099	broad.mit.edu	37	9	129596298	129596299	+	3'UTR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129596298_129596299delAA	uc004bql.2	+	3					ZBTB43_uc010mxf.2_3'UTR	NM_014007	NP_054726			zinc finger and BTB domain containing 43						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
GARNL3	84253	broad.mit.edu	37	9	130076035	130076035	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130076035delA	uc011mae.1	+						GARNL3_uc011mad.1_Intron	NM_032293	NP_115669			GTPase activating Rap/RanGAP domain-like 3						regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity|small GTPase regulator activity			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
GARNL3	84253	broad.mit.edu	37	9	130104367	130104367	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130104367delA	uc011mae.1	+						GARNL3_uc011mad.1_Intron|GARNL3_uc004bqt.1_Intron	NM_032293	NP_115669			GTPase activating Rap/RanGAP domain-like 3						regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity|small GTPase regulator activity			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	130156353	130156353	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130156353delG								GARNL3 (527 upstream) : SLC2A8 (3112 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	130156364	130156364	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130156364delA								GARNL3 (538 upstream) : SLC2A8 (3101 downstream)																																			---	---	---	---
ZNF79	7633	broad.mit.edu	37	9	130202000	130202000	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130202000delA	uc004bqw.3	+						ZNF79_uc011maf.1_Intron|ZNF79_uc011mag.1_Intron	NM_007135	NP_009066			zinc finger protein 79						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
C9orf117	286207	broad.mit.edu	37	9	130471694	130471695	+	Intron	INS	-	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130471694_130471695insC	uc004brn.1	+						PTRH1_uc004brm.2_Intron|C9orf117_uc010mxl.1_Intron	NM_001012502	NP_001012520			hypothetical protein LOC286207												0																		---	---	---	---
SH2D3C	10044	broad.mit.edu	37	9	130527708	130527708	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130527708delT	uc004bsc.2	-						SH2D3C_uc011mak.1_5'Flank|SH2D3C_uc004bsa.2_Intron|SH2D3C_uc004bsb.2_Intron	NM_170600	NP_733745			SH2 domain containing 3C isoform a						JNK cascade|small GTPase mediated signal transduction	cytoplasm|membrane	guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			ovary(1)	1																		---	---	---	---
GLE1	2733	broad.mit.edu	37	9	131275833	131275833	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131275833delA	uc004bvj.2	+						GLE1_uc004bvi.2_Intron|GLE1_uc010myd.2_Intron	NM_001003722	NP_001003722			GLE1 RNA export mediator homolog isoform 1						poly(A)+ mRNA export from nucleus|protein transport|transmembrane transport	cytoplasm|nuclear pore	protein binding				0																		---	---	---	---
NUP188	23511	broad.mit.edu	37	9	131721442	131721442	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131721442delT	uc004bws.1	+							NM_015354	NP_056169			nucleoporin 188kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|kidney(1)|breast(1)	7																		---	---	---	---
NUP188	23511	broad.mit.edu	37	9	131726644	131726646	+	Intron	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131726644_131726646delTTT	uc004bws.1	+							NM_015354	NP_056169			nucleoporin 188kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|kidney(1)|breast(1)	7																		---	---	---	---
FAM73B	84895	broad.mit.edu	37	9	131826492	131826493	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131826492_131826493delTT	uc004bxa.2	+						FAM73B_uc004bwy.2_Intron|FAM73B_uc004bwz.2_Intron|FAM73B_uc011mbn.1_Intron	NM_032809	NP_116198			hypothetical protein LOC84895							integral to membrane				skin(1)	1																		---	---	---	---
PPP2R4	5524	broad.mit.edu	37	9	131882705	131882706	+	Intron	DEL	AG	-	-	rs79351876		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131882705_131882706delAG	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	131920530	131920530	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131920530delT								PPP2R4 (9307 upstream) : IER5L (17301 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	132128516	132128517	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132128516_132128517insT								C9orf106 (43634 upstream) : C9orf50 (245989 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	132142035	132142035	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132142035delT								C9orf106 (57153 upstream) : C9orf50 (232471 downstream)																																			---	---	---	---
FNBP1	23048	broad.mit.edu	37	9	132671838	132671838	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132671838delA	uc004byw.1	-						FNBP1_uc011mbv.1_Intron|FNBP1_uc011mbw.1_Intron|FNBP1_uc004bza.2_Intron|FNBP1_uc004byz.1_Intron|FNBP1_uc011mbu.1_Intron|FNBP1_uc004byx.1_Intron|FNBP1_uc004byy.1_Intron	NM_015033	NP_055848			formin binding protein 1						endocytosis	cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|lysosome|plasma membrane	identical protein binding|lipid binding				0		Ovarian(14;0.000536)		GBM - Glioblastoma multiforme(294;0.0378)				T	MLL	AML								---	---	---	---
Unknown	0	broad.mit.edu	37	9	133436822	133436823	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133436822_133436823delTT								ASS1 (60162 upstream) : LOC100272217 (15916 downstream)																																			---	---	---	---
LAMC3	10319	broad.mit.edu	37	9	133909093	133909093	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133909093delC	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)														---	---	---	---
BAT2L1	84726	broad.mit.edu	37	9	134291502	134291502	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134291502delT	uc004cam.1	+											SubName: Full=BAT2L protein;								protein binding				0																		---	---	---	---
BAT2L1	84726	broad.mit.edu	37	9	134322049	134322049	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134322049delT	uc004can.3	+						BAT2L1_uc010mzj.1_5'Flank|BAT2L1_uc004cam.1_Intron	NM_013318	NP_037450			HLA-B associated transcript 2-like								protein binding				0																		---	---	---	---
MED27	9442	broad.mit.edu	37	9	134922940	134922940	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134922940delA	uc004cbe.1	-						MED27_uc004cbf.1_Intron|MED27_uc011mco.1_Intron|MED27_uc004cbg.3_Intron	NM_004269	NP_004260			mediator complex subunit 27						regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleolus|transcription factor complex	protein binding|transcription coactivator activity			skin(1)	1		Myeloproliferative disorder(178;0.206)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000193)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	135881616	135881616	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135881616delC								GFI1B (14533 upstream) : GTF3C5 (24446 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	136092364	136092365	+	IGR	DEL	AA	-	-	rs72120820		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136092364_136092365delAA								OBP2B (7736 upstream) : ABO (38198 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	136120135	136120139	+	IGR	DEL	TGTTT	-	-	rs111580263		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136120135_136120139delTGTTT								OBP2B (35507 upstream) : ABO (10424 downstream)																																			---	---	---	---
VAV2	7410	broad.mit.edu	37	9	136766233	136766234	+	Intron	INS	-	T	T	rs149037919	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136766233_136766234insT	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	137946296	137946297	+	IGR	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137946296_137946297delAG								FCN1 (136487 upstream) : OLFM1 (20792 downstream)																																			---	---	---	---
CAMSAP1	157922	broad.mit.edu	37	9	138718041	138718042	+	Intron	DEL	CA	-	-	rs60377963		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138718041_138718042delCA	uc004cgr.3	-						CAMSAP1_uc004cgq.3_Intron|CAMSAP1_uc010nbg.2_Intron	NM_015447	NP_056262			calmodulin regulated spectrin-associated protein							cytoplasm|microtubule				ovary(1)|central_nervous_system(1)|pancreas(1)	3				OV - Ovarian serous cystadenocarcinoma(145;1.4e-06)|Epithelial(140;1.11e-05)														---	---	---	---
NACC2	138151	broad.mit.edu	37	9	138908313	138908313	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138908313delG	uc004cgw.2	-						NACC2_uc010nbh.2_Intron	NM_144653	NP_653254			BTB (POZ) domain containing 14A						negative regulation of transcription, DNA-dependent|positive regulation of cell proliferation|protein homooligomerization	nuclear body					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	139073503	139073503	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139073503delA								C9orf69 (62772 upstream) : LHX3 (14595 downstream)																																			---	---	---	---
SNAPC4	6621	broad.mit.edu	37	9	139275544	139275544	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139275544delG	uc004chh.2	-							NM_003086	NP_003077			small nuclear RNA activating complex,						snRNA transcription from RNA polymerase II promoter|snRNA transcription from RNA polymerase III promoter	snRNA-activating protein complex	DNA binding|sequence-specific DNA binding transcription factor activity				0		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	139550056	139550056	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139550056delG	uc004cic.2	-											Homo sapiens HSPC324 mRNA, partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	139851121	139851147	+	IGR	DEL	ATGGATGGATGGATGGATGATGGGTGC	-	-	rs72332127		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139851121_139851147delATGGATGGATGGATGGATGATGGGTGC								LCN12 (1173 upstream) : PTGDS (18399 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	140020151	140020152	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140020151_140020152delAA								DPP7 (10956 upstream) : GRIN1 (13457 downstream)																																			---	---	---	---
CACNA1B	774	broad.mit.edu	37	9	140985780	140985780	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140985780delA	uc004cog.2	+						CACNA1B_uc004coi.2_Intron|CACNA1B_uc004cok.1_Intron|CACNA1B_uc010ncp.1_Intron	NM_000718	NP_000709			calcium channel, voltage-dependent, N type,						membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	ATP binding|protein C-terminus binding|voltage-gated calcium channel activity			breast(3)|large_intestine(2)|ovary(1)	6	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)													---	---	---	---
TUBBP5	643224	broad.mit.edu	37	9	141061827	141061828	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:141061827_141061828insA	uc010ncq.2	+							NR_027156				Homo sapiens cDNA, FLJ98407.												0																		---	---	---	---
DIP2C	22982	broad.mit.edu	37	10	680698	680698	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:680698delA	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)														---	---	---	---
LARP4B	23185	broad.mit.edu	37	10	920320	920320	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:920320delA	uc001ifs.1	-							NM_015155	NP_055970			La ribonucleoprotein domain family, member 4B								nucleotide binding|RNA binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
GTPBP4	23560	broad.mit.edu	37	10	1036226	1036227	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1036226_1036227delAA	uc001ift.2	+						GTPBP4_uc010qac.1_Intron|GTPBP4_uc001ifu.2_Intron|GTPBP4_uc010qad.1_Intron|GTPBP4_uc010qae.1_Intron	NM_012341	NP_036473			G protein-binding protein CRFG						negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of collagen binding|negative regulation of DNA replication|negative regulation of protein ubiquitination|protein stabilization|regulation of cyclin-dependent protein kinase activity|ribosome biogenesis	nucleolus|perinuclear region of cytoplasm	GTP binding|GTPase activity|protein binding			ovary(1)|skin(1)	2		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.0814)	Epithelial(11;0.0513)|all cancers(11;0.135)|OV - Ovarian serous cystadenocarcinoma(14;0.173)														---	---	---	---
IDI1	3422	broad.mit.edu	37	10	1098953	1098953	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1098953delT	uc001igc.2	-							NM_004508	NP_004499			isopentenyl-diphosphate delta isomerase						carotenoid biosynthetic process|cholesterol biosynthetic process	cytosol|peroxisome	hydrolase activity|isopentenyl-diphosphate delta-isomerase activity|metal ion binding				0		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.221)	Epithelial(11;0.0972)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	1956129	1956130	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1956129_1956130insT								ADARB2 (176411 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	3098143	3098143	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3098143delA								None (None upstream) : PFKP (11609 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	3330140	3330141	+	IGR	DEL	TA	-	-	rs34445964		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3330140_3330141delTA								PITRM1 (115137 upstream) : KLF6 (488048 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	3463129	3463150	+	Intron	DEL	GTAGGGTGCAGCTGGGACGCAA	-	-	rs113471012	byFrequency	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3463129_3463150delGTAGGGTGCAGCTGGGACGCAA	uc001igy.1	+											Homo sapiens cDNA clone IMAGE:5278070.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	3757799	3757800	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3757799_3757800delTT	uc001igy.1	+											Homo sapiens cDNA clone IMAGE:5278070.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	4299195	4299195	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4299195delT								KLF6 (471722 upstream) : LOC100216001 (322249 downstream)																																			---	---	---	---
AKR1C1	1645	broad.mit.edu	37	10	4970437	4970438	+	Intron	DEL	GA	-	-	rs71499613		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4970437_4970438delGA	uc001iho.2	+						AKR1E2_uc001ihl.1_Intron|AKR1C2_uc010qan.1_Intron	NM_001353	NP_001344			aldo-keto reductase family 1, member C1						bile acid and bile salt transport|bile acid metabolic process|cholesterol homeostasis|intestinal cholesterol absorption|protein homooligomerization|response to organophosphorus|xenobiotic metabolic process	cytosol	17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity|aldo-keto reductase (NADP) activity|androsterone dehydrogenase (B-specific) activity|bile acid binding|indanol dehydrogenase activity|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity			ovary(2)	2					NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	6796308	6796309	+	IGR	DEL	AT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6796308_6796309delAT								PRKCQ (174070 upstream) : SFMBT2 (407940 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	7017897	7017898	+	IGR	INS	-	AC	AC	rs141675623	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7017897_7017898insAC								PRKCQ (395659 upstream) : SFMBT2 (186351 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	7107624	7107625	+	IGR	DEL	TT	-	-	rs112020176		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7107624_7107625delTT								PRKCQ (485386 upstream) : SFMBT2 (96624 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	7110659	7110660	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7110659_7110660delTC								PRKCQ (488421 upstream) : SFMBT2 (93589 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	7725689	7725690	+	IGR	INS	-	A	A	rs148855745	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7725689_7725690insA								ITIH5 (16755 upstream) : ITIH2 (19546 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	8740679	8740680	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8740679_8740680insT								GATA3 (623517 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	9486726	9486727	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:9486726_9486727delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	9489463	9489463	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:9489463delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	10151429	10151430	+	IGR	INS	-	ACCT	ACCT	rs141400129	by1000genomes;by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10151429_10151430insACCT								None (None upstream) : SFTA1P (674972 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	10604889	10604891	+	IGR	DEL	TTT	-	-	rs113628740		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10604889_10604891delTTT								None (None upstream) : SFTA1P (221511 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	10821452	10821452	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10821452delT								None (None upstream) : SFTA1P (4950 downstream)																																			---	---	---	---
DHTKD1	55526	broad.mit.edu	37	10	12138647	12138647	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12138647delC	uc001ild.3	+							NM_018706	NP_061176			dehydrogenase E1 and transketolase domain						glycolysis	mitochondrion	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			ovary(1)|central_nervous_system(1)	2		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)															---	---	---	---
DHTKD1	55526	broad.mit.edu	37	10	12148116	12148116	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12148116delA	uc001ild.3	+							NM_018706	NP_061176			dehydrogenase E1 and transketolase domain						glycolysis	mitochondrion	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			ovary(1)|central_nervous_system(1)	2		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)															---	---	---	---
DHTKD1	55526	broad.mit.edu	37	10	12158397	12158397	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12158397delT	uc001ild.3	+							NM_018706	NP_061176			dehydrogenase E1 and transketolase domain						glycolysis	mitochondrion	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			ovary(1)|central_nervous_system(1)	2		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)															---	---	---	---
Unknown	0	broad.mit.edu	37	10	12327690	12327691	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12327690_12327691insT								CDC123 (35103 upstream) : CAMK1D (63892 downstream)																																			---	---	---	---
CAMK1D	57118	broad.mit.edu	37	10	12500880	12500882	+	Intron	DEL	TTT	-	-	rs150219433		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12500880_12500882delTTT	uc001ilo.2	+						CAMK1D_uc001iln.2_Intron	NM_153498	NP_705718			calcium/calmodulin-dependent protein kinase ID							calcium- and calmodulin-dependent protein kinase complex|cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)|stomach(1)	2				GBM - Glioblastoma multiforme(1;3.16e-05)														---	---	---	---
FRMD4A	55691	broad.mit.edu	37	10	13996782	13996783	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13996782_13996783insT	uc001ims.2	-						FRMD4A_uc009xjf.1_Intron|FRMD4A_uc001imt.1_Intron|FRMD4A_uc001imu.1_Intron	NM_018027	NP_060497			FERM domain containing 4A							cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3																		---	---	---	---
FRMD4A	55691	broad.mit.edu	37	10	14415756	14415756	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14415756delT	uc001imv.2	-						FRMD4A_uc001imw.1_Intron					Homo sapiens mRNA for KIAA1294 protein, partial cds.							cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3																		---	---	---	---
FAM107B	83641	broad.mit.edu	37	10	14594821	14594821	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14594821delA	uc001ina.1	-						FAM107B_uc010qbu.1_Intron|FAM107B_uc009xjg.1_Intron|FAM107B_uc001imy.1_Intron|FAM107B_uc001imz.1_Intron	NM_031453	NP_113641			hypothetical protein LOC83641											breast(4)	4																		---	---	---	---
DCLRE1C	64421	broad.mit.edu	37	10	14974635	14974635	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14974635delA	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					---	---	---	---
ITGA8	8516	broad.mit.edu	37	10	15617244	15617244	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15617244delC	uc001ioc.1	-						ITGA8_uc010qcb.1_Intron	NM_003638	NP_003629			integrin, alpha 8 precursor						cell differentiation|cell-cell adhesion|cell-matrix adhesion|integrin-mediated signaling pathway|nervous system development	integrin complex	receptor activity			ovary(3)|lung(3)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	16586209	16586209	+	IGR	DEL	A	-	-	rs113775578		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16586209delA								C1QL3 (22205 upstream) : RSU1 (46410 downstream)																																			---	---	---	---
RSU1	6251	broad.mit.edu	37	10	16815208	16815208	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16815208delA	uc001iok.2	-						RSU1_uc001iol.2_Intron|RSU1_uc001iom.2_Intron|RSU1_uc001ion.2_Intron	NM_152724	NP_689937			ras suppressor protein 1 isoform 2						cell junction assembly|signal transduction	cytosol	protein binding			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(1;7.54e-08)														---	---	---	---
RSU1	6251	broad.mit.edu	37	10	16820543	16820543	+	Intron	DEL	A	-	-	rs75336381		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16820543delA	uc001iok.2	-						RSU1_uc001iol.2_Intron|RSU1_uc001iom.2_Intron|RSU1_uc001ion.2_Intron	NM_152724	NP_689937			ras suppressor protein 1 isoform 2						cell junction assembly|signal transduction	cytosol	protein binding			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(1;7.54e-08)														---	---	---	---
CUBN	8029	broad.mit.edu	37	10	16873086	16873086	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16873086delA	uc001ioo.2	-							NM_001081	NP_001072			cubilin precursor						cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)													---	---	---	---
TRDMT1	1787	broad.mit.edu	37	10	17194110	17194110	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17194110delA	uc001iop.2	-						TRDMT1_uc001ioq.2_Intron|TRDMT1_uc001ior.2_Intron|TRDMT1_uc001ios.2_Intron|TRDMT1_uc009xjt.2_Intron|TRDMT1_uc010qcc.1_Intron	NM_004412	NP_004403			tRNA aspartic acid methyltransferase 1 isoform						tRNA processing	nucleus	DNA (cytosine-5-)-methyltransferase activity|DNA binding|RNA binding			ovary(1)	1																		---	---	---	---
ST8SIA6	338596	broad.mit.edu	37	10	17460225	17460225	+	Intron	DEL	T	-	-	rs113596114		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17460225delT	uc001ipd.2	-						ST8SIA6_uc010qce.1_Intron	NM_001004470	NP_001004470			ST8 alpha-N-acetyl-neuraminide						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	17663422	17663425	+	IGR	DEL	AAAA	-	-	rs67475058		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17663422_17663425delAAAA								PTPLA (4049 upstream) : STAM (22699 downstream)																																			---	---	---	---
MRC1	4360	broad.mit.edu	37	10	18183324	18183324	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18183324delT	uc001ipm.2	+							NM_002438	NP_002429			mannose receptor C type 1 precursor						receptor-mediated endocytosis	endosome membrane|integral to plasma membrane	mannose binding|receptor activity				0																		---	---	---	---
ARL5B	221079	broad.mit.edu	37	10	18964316	18964316	+	3'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18964316delT	uc001iqd.1	+	6					uc001iqe.2_5'Flank	NM_178815	NP_848930			ADP-ribosylation factor-like 8						small GTPase mediated signal transduction	intracellular	GTP binding			ovary(1)	1																		---	---	---	---
PLXDC2	84898	broad.mit.edu	37	10	20148209	20148210	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20148209_20148210insA	uc001iqg.1	+						PLXDC2_uc001iqh.1_Intron	NM_032812	NP_116201			plexin domain containing 2 precursor							integral to membrane				ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
PLXDC2	84898	broad.mit.edu	37	10	20194928	20194929	+	Intron	DEL	AA	-	-	rs146260310		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20194928_20194929delAA	uc001iqg.1	+						PLXDC2_uc001iqh.1_Intron	NM_032812	NP_116201			plexin domain containing 2 precursor							integral to membrane				ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
PLXDC2	84898	broad.mit.edu	37	10	20233901	20233901	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20233901delA	uc001iqg.1	+						PLXDC2_uc001iqh.1_Intron	NM_032812	NP_116201			plexin domain containing 2 precursor							integral to membrane				ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
PLXDC2	84898	broad.mit.edu	37	10	20361298	20361298	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20361298delA	uc001iqg.1	+						PLXDC2_uc001iqh.1_Intron	NM_032812	NP_116201			plexin domain containing 2 precursor							integral to membrane				ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
PLXDC2	84898	broad.mit.edu	37	10	20435380	20435383	+	Intron	DEL	CTTC	-	-	rs112918711		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20435380_20435383delCTTC	uc001iqg.1	+						PLXDC2_uc001iqh.1_Intron|PLXDC2_uc009xkc.1_Intron	NM_032812	NP_116201			plexin domain containing 2 precursor							integral to membrane				ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	20746920	20746920	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20746920delA								PLXDC2 (177805 upstream) : NEBL (321985 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	20844036	20844037	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20844036_20844037insT								PLXDC2 (274921 upstream) : NEBL (224868 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	20949375	20949376	+	IGR	DEL	TT	-	-	rs112320597		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20949375_20949376delTT								PLXDC2 (380260 upstream) : NEBL (119529 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	21691271	21691271	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21691271delG								NEBL (228155 upstream) : C10orf114 (92151 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	21732762	21732762	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21732762delA								NEBL (269646 upstream) : C10orf114 (50660 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	21791666	21791666	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21791666delA								C10orf114 (5453 upstream) : C10orf140 (10745 downstream)																																			---	---	---	---
MLLT10	8028	broad.mit.edu	37	10	21886788	21886789	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21886788_21886789insT	uc001iqs.2	+						MLLT10_uc001iqt.2_Intron|MLLT10_uc001iqv.2_Intron|MLLT10_uc001iqy.2_Intron|MLLT10_uc001iqz.2_Intron	NM_004641	NP_004632			myeloid/lymphoid or mixed-lineage leukemia						positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(1)|skin(1)	2								T	MLL|PICALM|CDK6	AL								---	---	---	---
DNAJC1	64215	broad.mit.edu	37	10	22138786	22138786	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22138786delA	uc001irc.2	-						DNAJC1_uc001ird.2_Intron	NM_022365	NP_071760			DnaJ (Hsp40) homolog, subfamily C, member 1						negative regulation of proteolysis|regulation of protein secretion|regulation of transcription, DNA-dependent	endoplasmic reticulum membrane|integral to membrane|microsome|nuclear membrane	ATPase activator activity|DNA binding|heat shock protein binding|unfolded protein binding			lung(1)	1		Breast(68;0.00869)|Prostate(175;0.0181)|Lung SC(717;0.0262)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	22427501	22427501	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22427501delT								DNAJC1 (134851 upstream) : COMMD3 (177798 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	22774724	22774725	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22774724_22774725delAC								SPAG6 (68186 upstream) : PIP4K2A (49042 downstream)																																			---	---	---	---
PIP4K2A	5305	broad.mit.edu	37	10	22867225	22867226	+	Intron	INS	-	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22867225_22867226insC	uc001irl.3	-						PIP4K2A_uc010qcu.1_Intron	NM_005028	NP_005019			phosphatidylinositol-5-phosphate 4-kinase, type								1-phosphatidylinositol-4-phosphate 5-kinase activity|1-phosphatidylinositol-5-phosphate 4-kinase activity|ATP binding			ovary(1)|skin(1)	2																		---	---	---	---
PIP4K2A	5305	broad.mit.edu	37	10	22976474	22976475	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22976474_22976475delAC	uc001irl.3	-							NM_005028	NP_005019			phosphatidylinositol-5-phosphate 4-kinase, type								1-phosphatidylinositol-4-phosphate 5-kinase activity|1-phosphatidylinositol-5-phosphate 4-kinase activity|ATP binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	23550167	23550168	+	IGR	INS	-	AC	AC	rs149725484	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23550167_23550168insAC								PTF1A (66988 upstream) : C10orf67 (55353 downstream)																																			---	---	---	---
KIAA1217	56243	broad.mit.edu	37	10	24026295	24026296	+	Intron	DEL	TT	-	-	rs10676755		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24026295_24026296delTT	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	24346010	24346010	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24346010delA	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	24498290	24498292	+	Intron	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24498290_24498292delAAA	uc001iru.3	+						KIAA1217_uc001irs.2_Intron|KIAA1217_uc001irt.3_Intron|KIAA1217_uc010qcy.1_Intron|KIAA1217_uc010qcz.1_Intron	NM_019590	NP_062536			sickle tail isoform 1						embryonic skeletal system development	cytoplasm				ovary(5)|skin(2)	7																		---	---	---	---
KIAA1217	56243	broad.mit.edu	37	10	24596710	24596710	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24596710delA	uc001iru.3	+						KIAA1217_uc001irs.2_Intron|KIAA1217_uc001irt.3_Intron|KIAA1217_uc010qcy.1_Intron|KIAA1217_uc010qcz.1_Intron|KIAA1217_uc001irv.1_Intron|KIAA1217_uc010qda.1_Intron	NM_019590	NP_062536			sickle tail isoform 1						embryonic skeletal system development	cytoplasm				ovary(5)|skin(2)	7																		---	---	---	---
PRTFDC1	56952	broad.mit.edu	37	10	25208796	25208796	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25208796delA	uc001ise.1	-						PRTFDC1_uc010qdd.1_Intron|PRTFDC1_uc001isf.1_Intron|PRTFDC1_uc009xkm.1_Intron	NM_020200	NP_064585			phosphoribosyl transferase domain containing 1						adenine salvage|central nervous system neuron development|cerebral cortex neuron differentiation|cytolysis|dendrite morphogenesis|GMP salvage|grooming behavior|hypoxanthine metabolic process|IMP salvage|lymphocyte proliferation|positive regulation of dopamine metabolic process|purine ribonucleoside salvage|response to amphetamine|striatum development	cytosol	hypoxanthine phosphoribosyltransferase activity|magnesium ion binding|nucleotide binding|protein homodimerization activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	26181903	26181904	+	IGR	DEL	AG	-	-	rs35213411		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26181903_26181904delAG								GPR158 (290748 upstream) : MYO3A (41098 downstream)																																			---	---	---	---
APBB1IP	54518	broad.mit.edu	37	10	26794357	26794357	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26794357delA	uc001iss.2	+						APBB1IP_uc009xks.1_Intron	NM_019043	NP_061916			amyloid beta (A4) precursor protein-binding,						blood coagulation|signal transduction	cytoskeleton|cytosol|focal adhesion|lamellipodium				lung(4)|skin(2)|central_nervous_system(1)	7																		---	---	---	---
ANKRD26	22852	broad.mit.edu	37	10	27324807	27324807	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27324807delA	uc001ith.2	-						ANKRD26_uc001itg.2_Intron|ANKRD26_uc009xku.1_Intron	NM_014915	NP_055730			ankyrin repeat domain 26							centrosome				large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|skin(1)	4																		---	---	---	---
YME1L1	10730	broad.mit.edu	37	10	27417520	27417520	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27417520delA	uc001iti.2	-						YME1L1_uc001itj.2_Intron|YME1L1_uc010qdl.1_Intron|YME1L1_uc009xkv.2_Intron	NM_139312	NP_647473			YME1-like 1 isoform 1						protein catabolic process|proteolysis	membrane|mitochondrion	ATP binding|metal ion binding|metalloendopeptidase activity|nucleoside-triphosphatase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	27716944	27716949	+	IGR	DEL	TGTTGA	-	-	rs71523578	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27716944_27716949delTGTTGA								PTCHD3 (13647 upstream) : RAB18 (76300 downstream)																																			---	---	---	---
ARMC4	55130	broad.mit.edu	37	10	28270269	28270269	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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	28578230	28578231	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28578230_28578231delAA	uc009xla.2	-						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	28608481	28608481	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28608481delA								MPP7 (16486 upstream) : WAC (212946 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	28765561	28765562	+	IGR	INS	-	T	T	rs113451733		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28765561_28765562insT								MPP7 (173566 upstream) : WAC (55865 downstream)																																			---	---	---	---
WAC	51322	broad.mit.edu	37	10	28824816	28824817	+	Intron	INS	-	T	T	rs144095892	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28824816_28824817insT	uc001iuf.2	+						WAC_uc001iud.2_Intron|WAC_uc001iue.2_Intron|WAC_uc009xlb.2_Intron|WAC_uc001iug.2_Intron|WAC_uc001iuh.2_Intron	NM_016628	NP_057712			WW domain-containing adapter with a coiled-coil						cell cycle checkpoint|histone H2B conserved C-terminal lysine ubiquitination|histone monoubiquitination|positive regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	nuclear speck	chromatin binding|RNA polymerase II core binding			large_intestine(1)|ovary(1)	2																		---	---	---	---
WAC	51322	broad.mit.edu	37	10	28906020	28906020	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28906020delA	uc001iuf.2	+						WAC_uc001iud.2_Intron|WAC_uc001iue.2_Intron|WAC_uc001iug.2_Intron|WAC_uc001iuh.2_Intron	NM_016628	NP_057712			WW domain-containing adapter with a coiled-coil						cell cycle checkpoint|histone H2B conserved C-terminal lysine ubiquitination|histone monoubiquitination|positive regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	nuclear speck	chromatin binding|RNA polymerase II core binding			large_intestine(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	28960761	28960762	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28960761_28960762insT								WAC (50840 upstream) : BAMBI (5662 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	28991021	28991021	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28991021delT								BAMBI (19153 upstream) : LYZL1 (586969 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	29107611	29107611	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29107611delT								BAMBI (135743 upstream) : LYZL1 (470379 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	29152557	29152558	+	IGR	INS	-	TG	TG	rs139021372	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29152557_29152558insTG								BAMBI (180689 upstream) : LYZL1 (425432 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	29158435	29158435	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29158435delA								BAMBI (186567 upstream) : LYZL1 (419555 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	29363301	29363302	+	IGR	INS	-	GA	GA	rs138146104	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29363301_29363302insGA								BAMBI (391433 upstream) : LYZL1 (214688 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	29373647	29373647	+	IGR	DEL	A	-	-	rs79637992		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29373647delA								BAMBI (401779 upstream) : LYZL1 (204343 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	29424445	29424445	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29424445delT								BAMBI (452577 upstream) : LYZL1 (153545 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	29531632	29531632	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29531632delG								BAMBI (559764 upstream) : LYZL1 (46358 downstream)																																			---	---	---	---
KIAA1462	57608	broad.mit.edu	37	10	30345448	30345448	+	Intron	DEL	T	-	-	rs78510036		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30345448delT	uc009xle.1	-						KIAA1462_uc001iuy.2_Intron|KIAA1462_uc001iuz.2_Intron	NM_020848	NP_065899			hypothetical protein LOC57608											ovary(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	30673204	30673204	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30673204delA								MTPAP (9827 upstream) : MAP3K8 (49662 downstream)																																			---	---	---	---
ZEB1	6935	broad.mit.edu	37	10	31716788	31716789	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31716788_31716789delAA	uc001ivs.3	+						ZEB1_uc001ivr.3_Intron|ZEB1_uc010qee.1_Intron|ZEB1_uc010qef.1_Intron|ZEB1_uc009xlh.1_Intron|ZEB1_uc009xli.1_Intron|ZEB1_uc009xlj.1_Intron|ZEB1_uc010qeg.1_Intron|ZEB1_uc009xlk.1_Intron|ZEB1_uc001ivt.3_Intron|ZEB1_uc001ivu.3_Intron|ZEB1_uc001ivv.3_Intron|ZEB1_uc010qeh.1_Intron|ZEB1_uc009xll.2_Intron|ZEB1_uc009xlm.1_Intron|ZEB1_uc009xln.1_Intron|ZEB1_uc009xlo.1_Intron|ZEB1_uc009xlp.2_Intron	NM_030751	NP_110378			zinc finger E-box binding homeobox 1 isoform b						cell proliferation|immune response|negative regulation of transcription from RNA polymerase II promoter|positive regulation of neuron differentiation	cytoplasm	E-box binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(3)|central_nervous_system(2)	5		Prostate(175;0.0156)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	31957060	31957060	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31957060delA								ZEB1 (138933 upstream) : ARHGAP12 (138165 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	32231150	32231150	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32231150delA								ARHGAP12 (13380 upstream) : KIF5B (66790 downstream)																																			---	---	---	---
KIF5B	3799	broad.mit.edu	37	10	32338661	32338662	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32338661_32338662delAA	uc001iwe.3	-							NM_004521	NP_004512			kinesin family member 5B						stress granule disassembly|vesicle transport along microtubule	kinesin complex|microtubule|perinuclear region of cytoplasm|vesicle	ATP binding|microtubule binding|microtubule motor activity		KIF5B/ALK(4)	lung(4)|ovary(1)	5		Prostate(175;0.0137)																---	---	---	---
PARD3	56288	broad.mit.edu	37	10	34983083	34983083	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34983083delA	uc010qej.1	-						PARD3_uc010qek.1_Intron|PARD3_uc010qel.1_Intron|PARD3_uc010qem.1_Intron|PARD3_uc010qen.1_Intron|PARD3_uc010qeo.1_Intron|PARD3_uc010qep.1_Intron|PARD3_uc010qeq.1_Intron|PARD3_uc001ixq.1_Intron|PARD3_uc001ixr.1_Intron|PARD3_uc001ixu.1_Intron	NM_019619	NP_062565			partitioning-defective protein 3 homolog						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)																---	---	---	---
PARD3	56288	broad.mit.edu	37	10	35019229	35019229	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35019229delT	uc010qej.1	-						PARD3_uc010qek.1_Intron|PARD3_uc010qel.1_Intron|PARD3_uc010qem.1_Intron|PARD3_uc010qen.1_Intron|PARD3_uc010qeo.1_Intron|PARD3_uc010qep.1_Intron|PARD3_uc010qeq.1_Intron|PARD3_uc001ixq.1_Intron|PARD3_uc001ixr.1_Intron|PARD3_uc001ixu.1_Intron	NM_019619	NP_062565			partitioning-defective protein 3 homolog						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)																---	---	---	---
CCNY	219771	broad.mit.edu	37	10	35745955	35745956	+	Intron	INS	-	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35745955_35745956insG	uc001iyw.3	+						CCNY_uc001iyu.3_Intron|CCNY_uc001iyv.3_Intron|CCNY_uc001iyx.3_Intron|CCNY_uc009xmb.2_Intron|CCNY_uc010qet.1_Intron	NM_145012	NP_659449			cyclin Y isoform 1						cell division|G2/M transition of mitotic cell cycle|positive regulation of cyclin-dependent protein kinase activity|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	cyclin-dependent protein kinase regulator activity|protein kinase binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	35884404	35884404	+	IGR	DEL	C	-	-	rs139171465		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35884404delC								CCNY (23559 upstream) : GJD4 (9934 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	36144975	36144976	+	IGR	INS	-	CCCT	CCCT	rs148108990	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36144975_36144976insCCCT								FZD8 (214613 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	36956106	36956106	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36956106delA								None (None upstream) : ANKRD30A (458679 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	38705105	38705105	+	IGR	DEL	T	-	-	rs75183298		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38705105delT								SEPT7L (13325 upstream) : LOC399744 (11969 downstream)																																			---	---	---	---
LOC399744	399744	broad.mit.edu	37	10	38727855	38727855	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38727855delA	uc009xme.2	+							NR_024497				Homo sapiens cDNA FLJ44672 fis, clone BRACE3006553.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	38869517	38869521	+	IGR	DEL	AAATG	-	-	rs113159018		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38869517_38869521delAAATG								LOC399744 (128437 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	38872577	38872581	+	IGR	DEL	TACCA	-	-	rs151129379	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38872577_38872581delTACCA								LOC399744 (131497 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	38939264	38939265	+	IGR	INS	-	AG	AG	rs142390219	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38939264_38939265insAG								LOC399744 (198184 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	38968755	38968756	+	IGR	INS	-	C	C	rs112830273		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38968755_38968756insC								LOC399744 (227675 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	38985722	38985722	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38985722delA								LOC399744 (244642 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	39090898	39090898	+	IGR	DEL	T	-	-	rs145632232		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:39090898delT								LOC399744 (349818 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	39141620	39141624	+	IGR	DEL	ACGAT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:39141620_39141624delACGAT								LOC399744 (400540 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42643206	42643206	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42643206delA								None (None upstream) : LOC441666 (184109 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42653302	42653303	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42653302_42653303insA								None (None upstream) : LOC441666 (174012 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42658052	42658052	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42658052delA								None (None upstream) : LOC441666 (169263 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42723665	42723669	+	IGR	DEL	TCATT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42723665_42723669delTCATT								None (None upstream) : LOC441666 (103646 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	43222945	43222945	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43222945delT								ZNF33B (88953 upstream) : BMS1 (55009 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	43245487	43245489	+	IGR	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43245487_43245489delTTT								ZNF33B (111495 upstream) : BMS1 (32465 downstream)																																			---	---	---	---
BMS1	9790	broad.mit.edu	37	10	43304863	43304864	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43304863_43304864delTT	uc001jaj.2	+							NM_014753	NP_055568			BMS1-like, ribosome assembly protein						ribosome assembly	nucleolus	ATP binding|GTP binding|GTPase activity			ovary(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
BMS1	9790	broad.mit.edu	37	10	43310526	43310527	+	Intron	INS	-	A	A	rs146360022		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43310526_43310527insA	uc001jaj.2	+							NM_014753	NP_055568			BMS1-like, ribosome assembly protein						ribosome assembly	nucleolus	ATP binding|GTP binding|GTPase activity			ovary(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
ZNF487	642819	broad.mit.edu	37	10	43974359	43974359	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43974359delT	uc010qfb.1	+							NR_026693				SubName: Full=cDNA FLJ52643, weakly similar to Zinc finger protein 11B;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	44489999	44490001	+	IGR	DEL	TCC	-	-	rs68064604		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44489999_44490001delTCC								HNRNPA3P1 (204134 upstream) : CXCL12 (375606 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	45000450	45000450	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45000450delA								CXCL12 (119908 upstream) : TMEM72 (406314 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	45346465	45346466	+	Intron	INS	-	TG	TG	rs146967412	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45346465_45346466insTG	uc001jbk.1	-						uc001jbl.2_Intron					Homo sapiens cDNA FLJ31956 fis, clone NT2RP7007359.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	45508563	45508563	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45508563delC	uc001jbx.1	-											Homo sapiens zinc finger protein 22 (KOX 15), mRNA (cDNA clone IMAGE:4826621).																														---	---	---	---
ALOX5	240	broad.mit.edu	37	10	45905087	45905087	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45905087delT	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	46017929	46017929	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46017929delC	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	46985613	46985613	+	IGR	DEL	T	-	-	rs77607175		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46985613delT								SYT15 (15012 upstream) : GPRIN2 (7933 downstream)																																			---	---	---	---
ANXA8	653145	broad.mit.edu	37	10	47021225	47021225	+	Intron	DEL	C	-	-	rs9330488	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47021225delC	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	47078724	47078735	+	Intron	DEL	TTCTTTTTTTTT	-	-	rs71846441		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47078724_47078735delTTCTTTTTTTTT	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	47093884	47093885	+	Intron	INS	-	C	C	rs61142233	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47093884_47093885insC	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	47106752	47106752	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47106752delG	uc001jed.3	-						uc001jef.2_Intron					Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3																		---	---	---	---
ANXA8	653145	broad.mit.edu	37	10	47129045	47129045	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47129045delA	uc001jed.3	-						uc001jef.2_Intron					Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3																		---	---	---	---
FAM35B2	439965	broad.mit.edu	37	10	47416689	47416689	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47416689delA	uc010qga.1	+						FAM35B2_uc010qfz.1_Intron					SubName: Full=cDNA FLJ59018, highly similar to Protein FAM35A;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	48567722	48567723	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48567722_48567723insA								GDF10 (128556 upstream) : FRMPD2L1 (276320 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	48595473	48595473	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48595473delC								GDF10 (156307 upstream) : FRMPD2L1 (248570 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	48872114	48872114	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48872114delA								FRMPD2L1 (8482 upstream) : FRMPD2 (492494 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	48980053	48980053	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48980053delA	uc001jgc.1	+											full-length cDNA clone CS0DI009YC01 of Placenta Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
C10orf72	196740	broad.mit.edu	37	10	50256688	50256688	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50256688delA	uc001jhf.2	-							NM_001031746	NP_001026916			hypothetical protein LOC196740 isoform 1							integral to membrane|plasma membrane					0																		---	---	---	---
PARG	8505	broad.mit.edu	37	10	51054793	51054794	+	Intron	DEL	TG	-	-	rs71668837		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51054793_51054794delTG	uc001jif.2	-						PARG_uc001jih.2_Intron|PARG_uc001jig.2_Intron|PARG_uc010qgv.1_Intron|PARG_uc009xoi.2_Intron|PARG_uc010qgw.1_Intron|PARG_uc009xoj.2_Intron|PARG_uc010qgx.1_Intron	NM_003631	NP_003622			poly (ADP-ribose) glycohydrolase						carbohydrate metabolic process	nucleus	poly(ADP-ribose) glycohydrolase activity			ovary(2)	2				Epithelial(53;0.213)														---	---	---	---
AGAP6	414189	broad.mit.edu	37	10	51763958	51763958	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51763958delA	uc001jix.3	+							NM_001077665	NP_001071133			ArfGAP with GTPase domain, ankyrin repeat and PH						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			skin(1)	1																		---	---	---	---
SGMS1	259230	broad.mit.edu	37	10	52330676	52330677	+	Intron	INS	-	A	A	rs147700120	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52330676_52330677insA	uc001jje.2	-						SGMS1_uc010qhk.1_Intron|SGMS1_uc009xot.1_Intron|SGMS1_uc009xou.1_Intron	NM_147156	NP_671512			sphingomyelin synthase 1						apoptosis|cell growth|sphingomyelin biosynthetic process	endoplasmic reticulum|Golgi trans cisterna|integral to Golgi membrane|nucleus|plasma membrane	ceramide cholinephosphotransferase activity|kinase activity|sphingomyelin synthase activity			ovary(1)|kidney(1)	2																		---	---	---	---
PRKG1	5592	broad.mit.edu	37	10	53713481	53713482	+	Intron	INS	-	T	T	rs116690314	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53713481_53713482insT	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	54714996	54714999	+	IGR	DEL	AGAT	-	-	rs57676258		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54714996_54714999delAGAT								MBL2 (183536 upstream) : PCDH15 (847536 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	54748887	54748888	+	IGR	INS	-	CT	CT			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54748887_54748888insCT								MBL2 (217427 upstream) : PCDH15 (813647 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	55348001	55348001	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55348001delT								MBL2 (816541 upstream) : PCDH15 (214534 downstream)																																			---	---	---	---
PCDH15	65217	broad.mit.edu	37	10	55949051	55949051	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55949051delA	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	55993293	55993293	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55993293delG	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	56780144	56780145	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:56780144_56780145delAA	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	56914856	56914856	+	Intron	DEL	T	-	-	rs78653883		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:56914856delT	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	56918645	56918646	+	Intron	DEL	AG	-	-	rs35343114		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:56918645_56918646delAG	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	57461529	57461529	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:57461529delA								PCDH15 (73827 upstream) : ZWINT (655670 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	57576674	57576674	+	IGR	DEL	T	-	-	rs139221176		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:57576674delT								PCDH15 (188972 upstream) : ZWINT (540525 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	58488089	58488090	+	IGR	INS	-	CA	CA	rs118094572		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:58488089_58488090insCA								ZWINT (367055 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	59651997	59651998	+	IGR	INS	-	AG	AG	rs150908236	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:59651997_59651998insAG								None (None upstream) : IPMK (303620 downstream)																																			---	---	---	---
UBE2D1	7321	broad.mit.edu	37	10	60109966	60109966	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60109966delG	uc001jke.1	+							NM_003338	NP_003329			ubiquitin-conjugating enzyme E2D 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|BMP signaling pathway|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K48-linked ubiquitination|transforming growth factor beta receptor signaling pathway	cytosol|nucleoplasm	ATP binding|protein binding|ubiquitin-protein ligase activity			skin(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	60864443	60864444	+	IGR	INS	-	GATA	GATA	rs34543631		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60864443_60864444insGATA								BICC1 (275598 upstream) : PHYHIPL (71904 downstream)																																			---	---	---	---
PHYHIPL	84457	broad.mit.edu	37	10	60993190	60993190	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60993190delT	uc001jkk.3	+						PHYHIPL_uc001jkl.3_Intron|PHYHIPL_uc001jkm.3_Intron	NM_032439	NP_115815			phytanoyl-CoA 2-hydroxylase interacting												0																		---	---	---	---
ANK3	288	broad.mit.edu	37	10	61815229	61815229	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61815229delT	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	61951144	61951144	+	Intron	DEL	A	-	-	rs111768554		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61951144delA	uc001jky.2	-						ANK3_uc010qih.1_Intron|ANK3_uc001jkz.3_Intron|ANK3_uc001jlb.1_Intron|ANK3_uc001jlc.1_Intron	NM_020987	NP_066267			ankyrin 3 isoform 1						establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19																		---	---	---	---
ANK3	288	broad.mit.edu	37	10	62420677	62420678	+	Intron	DEL	CA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:62420677_62420678delCA	uc001jkz.3	-							NM_001149	NP_001140			ankyrin 3 isoform 2						establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19																		---	---	---	---
ZNF365	22891	broad.mit.edu	37	10	64265372	64265372	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64265372delT	uc001jmc.2	+							NM_199451	NP_955523			zinc finger protein 365 isoform C											ovary(1)|skin(1)	2	Prostate(12;0.0297)|all_hematologic(501;0.228)																	---	---	---	---
ZNF365	22891	broad.mit.edu	37	10	64323085	64323086	+	Intron	DEL	GC	-	-	rs35797046	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64323085_64323086delGC	uc001jmd.1	+						ZNF365_uc001jmc.2_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)																	---	---	---	---
ZNF365	22891	broad.mit.edu	37	10	64393100	64393100	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64393100delT	uc001jmd.1	+						ZNF365_uc001jmc.2_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	64923515	64923515	+	IGR	DEL	T	-	-	rs78959322		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64923515delT								NRBF2 (8730 upstream) : JMJD1C (3475 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	66070523	66070523	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66070523delA								REEP3 (688552 upstream) : ANXA2P3 (514762 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	66337158	66337158	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66337158delC								REEP3 (955187 upstream) : ANXA2P3 (248127 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	66912654	66912654	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66912654delC								ANXA2P3 (326020 upstream) : CTNNA3 (767071 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	66937597	66937598	+	IGR	INS	-	T	T	rs148313183	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66937597_66937598insT								ANXA2P3 (350963 upstream) : CTNNA3 (742127 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	67616441	67616441	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67616441delA								None (None upstream) : CTNNA3 (63284 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	67629571	67629571	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67629571delA								None (None upstream) : CTNNA3 (50154 downstream)																																			---	---	---	---
HERC4	26091	broad.mit.edu	37	10	69794579	69794579	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69794579delT	uc001jng.3	-						HERC4_uc001jnf.3_Intron|HERC4_uc001jnh.3_Intron|HERC4_uc009xpr.2_Intron|HERC4_uc001jni.3_Intron|HERC4_uc001jnj.2_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																		---	---	---	---
PBLD	64081	broad.mit.edu	37	10	70058515	70058524	+	Intron	DEL	ACACACACAC	-	-	rs113959367		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70058515_70058524delACACACACAC	uc001jns.1	-						PBLD_uc001jnr.1_5'Flank|PBLD_uc001jnt.1_Intron|PBLD_uc001jnu.1_Intron|PBLD_uc001jnv.1_Intron	NM_022129	NP_071412			MAWD binding protein isoform a						biosynthetic process		isomerase activity			skin(2)|ovary(1)	3																		---	---	---	---
PBLD	64081	broad.mit.edu	37	10	70082662	70082662	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70082662delA	uc001jns.1	-						PBLD_uc001jnt.1_Intron|PBLD_uc001jnu.1_Intron	NM_022129	NP_071412			MAWD binding protein isoform a						biosynthetic process		isomerase activity			skin(2)|ovary(1)	3																		---	---	---	---
RUFY2	55680	broad.mit.edu	37	10	70140858	70140858	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70140858delA	uc001job.2	-						RUFY2_uc001jnz.1_Intron|RUFY2_uc001joc.2_Intron|RUFY2_uc010qiw.1_Intron|RUFY2_uc001jod.1_Intron	NM_017987	NP_060457			RUN and FYVE domain-containing 2 isoform a							nucleus	metal ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	70172751	70172751	+	IGR	DEL	G	-	-	rs4746767	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70172751delG								RUFY2 (5700 upstream) : DNA2 (1071 downstream)																																			---	---	---	---
CCAR1	55749	broad.mit.edu	37	10	70530835	70530835	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70530835delA	uc001joo.2	+						CCAR1_uc001jol.1_Intron|CCAR1_uc001jom.1_Intron|CCAR1_uc009xpx.1_Intron|CCAR1_uc001jon.1_Intron|CCAR1_uc010qiz.1_Intron|CCAR1_uc010qja.1_Intron|CCAR1_uc010qjb.1_Intron	NM_018237	NP_060707			cell-cycle and apoptosis regulatory protein 1						apoptosis|cell cycle|nuclear mRNA splicing, via spliceosome|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm|perinuclear region of cytoplasm	calcium ion binding|nucleic acid binding|protein binding			ovary(6)|large_intestine(1)	7																		---	---	---	---
CCAR1	55749	broad.mit.edu	37	10	70548673	70548673	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70548673delT	uc001joo.2	+						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																		---	---	---	---
HK1	3098	broad.mit.edu	37	10	71085597	71085597	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71085597delT	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																		---	---	---	---
TYSND1	219743	broad.mit.edu	37	10	71906567	71906567	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71906567delT	uc001jqr.2	-						TYSND1_uc001jqq.2_5'Flank|TYSND1_uc001jqs.2_5'Flank|TYSND1_uc001jqt.2_5'Flank	NM_173555	NP_775826			trypsin domain containing 1 isoform a						proteolysis	peroxisome	serine-type endopeptidase activity			large_intestine(1)	1																OREG0020235	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TYSND1	219743	broad.mit.edu	37	10	71908774	71908775	+	5'Flank	INS	-	C	C	rs142462347	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71908774_71908775insC	uc001jqr.2	-						TYSND1_uc001jqq.2_5'Flank|TYSND1_uc001jqs.2_5'Flank|TYSND1_uc001jqt.2_5'Flank	NM_173555	NP_775826			trypsin domain containing 1 isoform a						proteolysis	peroxisome	serine-type endopeptidase activity			large_intestine(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	72345385	72345386	+	IGR	INS	-	TGTA	TGTA	rs144365033	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72345385_72345386insTGTA								KIAA1274 (17180 upstream) : PRF1 (11719 downstream)																																			---	---	---	---
SGPL1	8879	broad.mit.edu	37	10	72613341	72613341	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72613341delT	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)													---	---	---	---
PCBD1	5092	broad.mit.edu	37	10	72644720	72644720	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72644720delT	uc001jrn.1	-							NM_000281	NP_000272			pterin-4 alpha-carbinolamine						L-phenylalanine catabolic process|regulation of transcription, DNA-dependent|tetrahydrobiopterin biosynthetic process|transcription, DNA-dependent	cytosol|nucleus	4-alpha-hydroxytetrahydrobiopterin dehydratase activity|identical protein binding|transcription coactivator activity				0																		---	---	---	---
UNC5B	219699	broad.mit.edu	37	10	72984011	72984012	+	Intron	INS	-	AC	AC	rs140760302	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72984011_72984012insAC	uc001jro.2	+						UNC5B_uc001jrp.2_Intron	NM_170744	NP_734465			unc-5 homolog B precursor						apoptosis|axon guidance|regulation of apoptosis	integral to membrane				ovary(2)|lung(1)	3																		---	---	---	---
UNC5B	219699	broad.mit.edu	37	10	72991406	72991407	+	Intron	DEL	TT	-	-	rs113129554		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72991406_72991407delTT	uc001jro.2	+						UNC5B_uc001jrp.2_Intron	NM_170744	NP_734465			unc-5 homolog B precursor						apoptosis|axon guidance|regulation of apoptosis	integral to membrane				ovary(2)|lung(1)	3																		---	---	---	---
CDH23	64072	broad.mit.edu	37	10	73163284	73163284	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73163284delT	uc001jrx.3	+						CDH23_uc001jrw.3_Intron|CDH23_uc001jrv.2_Intron|CDH23_uc009xql.2_Intron	NM_022124	NP_071407			cadherin-like 23 isoform 1 precursor						calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11																		---	---	---	---
CDH23	64072	broad.mit.edu	37	10	73344690	73344690	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73344690delG	uc001jrx.3	+						CDH23_uc001jrw.3_Intron|CDH23_uc009xql.2_Intron	NM_022124	NP_071407			cadherin-like 23 isoform 1 precursor						calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11																		---	---	---	---
CDH23	64072	broad.mit.edu	37	10	73405773	73405773	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73405773delG	uc001jrx.3	+						CDH23_uc001jrw.3_Intron|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																		---	---	---	---
CDH23	64072	broad.mit.edu	37	10	73457429	73457429	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73457429delA	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																		---	---	---	---
CHST3	9469	broad.mit.edu	37	10	73740218	73740218	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73740218delA	uc001jsn.2	+							NM_004273	NP_004264			chondroitin 6-sulfotransferase 3						chondroitin sulfate biosynthetic process	Golgi membrane|integral to membrane	chondroitin 6-sulfotransferase activity				0																		---	---	---	---
CCDC109A	90550	broad.mit.edu	37	10	74625522	74625522	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74625522delT	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)																	---	---	---	---
PLA2G12B	84647	broad.mit.edu	37	10	74705412	74705414	+	Intron	DEL	TTT	-	-	rs113655052	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74705412_74705414delTTT	uc001jtf.1	-						PLA2G12B_uc009xqt.1_Intron|PLA2G12B_uc010qjz.1_Intron	NM_032562	NP_115951			phospholipase A2, group XIIB precursor						lipid catabolic process	extracellular region	calcium ion binding|phospholipase A2 activity			ovary(1)	1	Prostate(51;0.0198)																	---	---	---	---
NUDT13	25961	broad.mit.edu	37	10	74889738	74889739	+	Intron	DEL	AA	-	-	rs75712972		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74889738_74889739delAA	uc001jtj.2	+						NUDT13_uc010qkc.1_Intron|NUDT13_uc010qkd.1_Intron|NUDT13_uc009xqw.2_Intron|NUDT13_uc001jtk.2_Intron|NUDT13_uc010qke.1_Intron|NUDT13_uc001jtl.2_Intron	NM_015901	NP_056985			nudix-type motif 13								hydrolase activity|metal ion binding				0	Prostate(51;0.0119)																	---	---	---	---
FAM149B1	317662	broad.mit.edu	37	10	74930548	74930549	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74930548_74930549delAA	uc009xqz.2	+						FAM149B1_uc010qkf.1_Intron|ECD_uc009xqx.2_5'Flank|ECD_uc001jtn.2_5'Flank|ECD_uc009xqy.2_5'Flank|ECD_uc001jto.2_5'Flank	NM_173348	NP_775483			hypothetical protein LOC317662												0																		---	---	---	---
AP3M1	26985	broad.mit.edu	37	10	75891805	75891806	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75891805_75891806insT	uc001jwf.2	-						AP3M1_uc001jwg.2_Intron|AP3M1_uc001jwh.2_Intron|AP3M1_uc010qla.1_Intron	NM_207012	NP_996895			adaptor-related protein complex 3, mu 1 subunit						protein targeting to lysosome|vesicle-mediated transport	clathrin adaptor complex|Golgi apparatus|lysosome	protein binding				0	Prostate(51;0.0112)																	---	---	---	---
ADK	132	broad.mit.edu	37	10	76229733	76229734	+	Intron	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76229733_76229734delTC	uc001jwi.2	+						ADK_uc010qlb.1_Intron|ADK_uc001jwj.2_Intron|ADK_uc010qlc.1_Intron	NM_006721	NP_006712			adenosine kinase isoform b						purine base metabolic process|purine ribonucleoside salvage	cytosol	adenosine kinase activity|ATP binding|metal ion binding|phosphotransferase activity, alcohol group as acceptor			ovary(1)|skin(1)	2	Prostate(51;0.0112)|Ovarian(15;0.148)				Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Pegademase bovine(DB00061)|Ribavirin(DB00811)													---	---	---	---
ADK	132	broad.mit.edu	37	10	76395849	76395849	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76395849delA	uc001jwi.2	+						ADK_uc010qlb.1_Intron|ADK_uc001jwj.2_Intron|ADK_uc010qlc.1_Intron|ADK_uc001jwl.2_Intron	NM_006721	NP_006712			adenosine kinase isoform b						purine base metabolic process|purine ribonucleoside salvage	cytosol	adenosine kinase activity|ATP binding|metal ion binding|phosphotransferase activity, alcohol group as acceptor			ovary(1)|skin(1)	2	Prostate(51;0.0112)|Ovarian(15;0.148)				Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Pegademase bovine(DB00061)|Ribavirin(DB00811)													---	---	---	---
ADK	132	broad.mit.edu	37	10	76462328	76462329	+	Intron	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76462328_76462329delTC	uc001jwi.2	+						ADK_uc010qlb.1_Intron|ADK_uc001jwj.2_Intron|ADK_uc010qlc.1_Intron|ADK_uc001jwl.2_Intron	NM_006721	NP_006712			adenosine kinase isoform b						purine base metabolic process|purine ribonucleoside salvage	cytosol	adenosine kinase activity|ATP binding|metal ion binding|phosphotransferase activity, alcohol group as acceptor			ovary(1)|skin(1)	2	Prostate(51;0.0112)|Ovarian(15;0.148)				Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Pegademase bovine(DB00061)|Ribavirin(DB00811)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	77154477	77154477	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77154477delG								COMTD1 (158707 upstream) : ZNF503 (3128 downstream)																																			---	---	---	---
C10orf11	83938	broad.mit.edu	37	10	78105688	78105689	+	Intron	INS	-	A	A	rs142051281	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78105688_78105689insA	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	78731733	78731734	+	Intron	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78731733_78731734delGT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	79976803	79976806	+	IGR	DEL	GTGC	-	-	rs67718148		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79976803_79976806delGTGC								RPS24 (160233 upstream) : LOC283050 (726278 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	80244761	80244761	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80244761delT	uc010qlp.1	+											SubName: Full=cDNA FLJ57363;																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	80244762	80244763	+	Intron	INS	-	T	T	rs79435027		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80244762_80244763insT	uc010qlp.1	+											SubName: Full=cDNA FLJ57363;																														---	---	---	---
MBL1P	8512	broad.mit.edu	37	10	81680656	81680656	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81680656delA	uc001kbf.2	+						MBL1P_uc001kbg.1_RNA					Homo sapiens mannose-binding protein-A pseudogene (MBL1P1) mRNA sequence.												0																		---	---	---	---
ANXA11	311	broad.mit.edu	37	10	81916277	81916277	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81916277delT	uc001kbq.1	-						ANXA11_uc010qlx.1_Intron|ANXA11_uc001kbr.1_Intron|ANXA11_uc001kbs.1_Intron|ANXA11_uc001kbt.1_Intron|ANXA11_uc010qly.1_Intron|ANXA11_uc009xsq.1_Intron|ANXA11_uc001kbu.1_Intron	NM_145869	NP_665876			annexin A11						cell cycle|cytokinesis, completion of separation|phagocytosis|response to calcium ion	azurophil granule|melanosome|midbody|nuclear envelope|nucleoplasm|phagocytic vesicle|specific granule|spindle	calcium-dependent phospholipid binding|calcium-dependent protein binding|S100 alpha binding			ovary(1)	1	Prostate(51;0.00985)|all_epithelial(25;0.0951)		Colorectal(32;0.109)															---	---	---	---
Unknown	0	broad.mit.edu	37	10	82152460	82152460	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82152460delT								DYDC2 (24631 upstream) : C10orf58 (15782 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	82152462	82152463	+	IGR	DEL	TA	-	-	rs7907298	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82152462_82152463delTA								DYDC2 (24633 upstream) : C10orf58 (15779 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	82768370	82768371	+	IGR	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82768370_82768371delAG								SH2D4B (362054 upstream) : NRG3 (866699 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	83453391	83453392	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:83453391_83453392delTG								None (None upstream) : NRG3 (181678 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	85517343	85517344	+	IGR	INS	-	AC	AC	rs147916303	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85517343_85517344insAC								NRG3 (770408 upstream) : GHITM (381841 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	85708023	85708024	+	IGR	INS	-	AG	AG			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85708023_85708024insAG								NRG3 (961088 upstream) : GHITM (191161 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	85855771	85855774	+	IGR	DEL	CCTC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85855771_85855774delCCTC								None (None upstream) : GHITM (43411 downstream)																																			---	---	---	---
GHITM	27069	broad.mit.edu	37	10	85912265	85912265	+	3'UTR	DEL	T	-	-	rs1064705		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85912265delT	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	86497009	86497009	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86497009delA								FAM190B (218733 upstream) : GRID1 (862303 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	86953389	86953390	+	RNA	INS	-	TG	TG	rs150413984	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86953389_86953390insTG	uc001kdj.1	-	4		c.1834_1835insCA								Homo sapiens cDNA FLJ40305 fis, clone TESTI2029244.																														---	---	---	---
GRID1	2894	broad.mit.edu	37	10	87386914	87386914	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87386914delA	uc001kdl.1	-						GRID1_uc009xsu.1_Intron|GRID1_uc010qmf.1_Intron	NM_017551	NP_060021			glutamate receptor, ionotropic, delta 1							cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(5)|upper_aerodigestive_tract(2)|large_intestine(2)|central_nervous_system(1)	10					L-Glutamic Acid(DB00142)										Multiple Myeloma(13;0.14)			---	---	---	---
GRID1	2894	broad.mit.edu	37	10	87797475	87797475	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87797475delA	uc001kdl.1	-						GRID1_uc009xsu.1_Intron	NM_017551	NP_060021			glutamate receptor, ionotropic, delta 1							cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(5)|upper_aerodigestive_tract(2)|large_intestine(2)|central_nervous_system(1)	10					L-Glutamic Acid(DB00142)										Multiple Myeloma(13;0.14)			---	---	---	---
GRID1	2894	broad.mit.edu	37	10	88035029	88035029	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88035029delA	uc001kdl.1	-						GRID1_uc009xsu.1_Intron	NM_017551	NP_060021			glutamate receptor, ionotropic, delta 1							cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(5)|upper_aerodigestive_tract(2)|large_intestine(2)|central_nervous_system(1)	10					L-Glutamic Acid(DB00142)										Multiple Myeloma(13;0.14)			---	---	---	---
Unknown	0	broad.mit.edu	37	10	88805871	88805871	+	IGR	DEL	T	-	-	rs75464240		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88805871delT								AGAP11 (21385 upstream) : GLUD1 (4375 downstream)																																			---	---	---	---
PAPSS2	9060	broad.mit.edu	37	10	89498175	89498176	+	Intron	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89498175_89498176delTG	uc001kex.2	+						PAPSS2_uc001kew.2_Intron	NM_004670	NP_004661			3'-phosphoadenosine 5'-phosphosulfate synthase 2						3'-phosphoadenosine 5'-phosphosulfate biosynthetic process|skeletal system development|sulfate assimilation|xenobiotic metabolic process	cytosol	adenylylsulfate kinase activity|ATP binding|protein binding|sulfate adenylyltransferase (ATP) activity			central_nervous_system(1)|skin(1)	2		Melanoma(5;0.019)|Colorectal(252;0.123)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00164)|Colorectal(12;0.000323)|COAD - Colon adenocarcinoma(12;0.00124)														---	---	---	---
CFLP1	142913	broad.mit.edu	37	10	89593414	89593414	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89593414delT	uc001kfa.2	+											Homo sapiens cofilin pseudogene 1, mRNA (cDNA clone IMAGE:5168640).												0																		---	---	---	---
STAMBPL1	57559	broad.mit.edu	37	10	90652111	90652112	+	Intron	DEL	GT	-	-	rs112774452		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90652111_90652112delGT	uc001kfk.2	+						STAMBPL1_uc010qmx.1_Intron|STAMBPL1_uc009xto.2_RNA	NM_020799	NP_065850			STAM binding protein-like 1								metal ion binding|metallopeptidase activity|protein binding			ovary(1)	1		Colorectal(252;0.0381)		Colorectal(12;6.38e-05)|COAD - Colon adenocarcinoma(12;7.75e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	90839266	90839266	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90839266delA								FAS (63725 upstream) : CH25H (126430 downstream)																																			---	---	---	---
SLC16A12	387700	broad.mit.edu	37	10	91242864	91242864	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91242864delT	uc001kgm.2	-							NM_213606	NP_998771			solute carrier family 16 (monocarboxylic acid							integral to membrane|plasma membrane	symporter activity			skin(1)	1																		---	---	---	---
KIF20B	9585	broad.mit.edu	37	10	91497021	91497021	+	Intron	DEL	T	-	-	rs72076248		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91497021delT	uc001kgs.1	+						KIF20B_uc001kgr.1_Intron|KIF20B_uc001kgt.1_Intron|KIF20B_uc009xtw.1_5'Flank	NM_016195	NP_057279			M-phase phosphoprotein 1						cell cycle arrest|cell division|microtubule-based movement|mitosis|regulation of mitosis	centrosome|microtubule|nucleolus|nucleoplasm|spindle	ATP binding|ATPase activity|microtubule motor activity|WW domain binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
HTR7	3363	broad.mit.edu	37	10	92575492	92575492	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92575492delA	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	92691339	92691340	+	IGR	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92691339_92691340delGT								ANKRD1 (10307 upstream) : NUDT9P1 (220421 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	92865878	92865878	+	IGR	DEL	C	-	-	rs139525981		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92865878delC								ANKRD1 (184846 upstream) : NUDT9P1 (45883 downstream)																																			---	---	---	---
PCGF5	84333	broad.mit.edu	37	10	93006723	93006734	+	Intron	DEL	GATAGATAGATA	-	-	rs72134127		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93006723_93006734delGATAGATAGATA	uc001khh.2	+						PCGF5_uc010qnk.1_Intron|PCGF5_uc001khi.2_Intron	NM_032373	NP_115749			polycomb group ring finger 5						regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|PcG protein complex	zinc ion binding			lung(1)	1																		---	---	---	---
TNKS2	80351	broad.mit.edu	37	10	93597985	93597985	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93597985delG	uc001khp.2	+							NM_025235	NP_079511			tankyrase, TRF1-interacting ankyrin-related						positive regulation of canonical Wnt receptor signaling pathway|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein polyubiquitination|Wnt receptor signaling pathway	Golgi membrane|microsome|nuclear envelope|pericentriolar material|perinuclear region of cytoplasm	NAD+ ADP-ribosyltransferase activity|protein binding			kidney(3)|skin(3)|ovary(1)|lung(1)	8		Colorectal(252;0.162)																---	---	---	---
BTAF1	9044	broad.mit.edu	37	10	93713829	93713829	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93713829delT	uc001khr.2	+						BTAF1_uc009xua.1_Intron|BTAF1_uc001khs.1_5'Flank	NM_003972	NP_003963			BTAF1 RNA polymerase II, B-TFIID transcription						negative regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0846)																---	---	---	---
BTAF1	9044	broad.mit.edu	37	10	93748896	93748896	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93748896delT	uc001khr.2	+						BTAF1_uc001khs.1_Intron|BTAF1_uc001kht.1_Intron	NM_003972	NP_003963			BTAF1 RNA polymerase II, B-TFIID transcription						negative regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0846)																---	---	---	---
BTAF1	9044	broad.mit.edu	37	10	93773991	93773991	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93773991delT	uc001khr.2	+							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	93897757	93897757	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93897757delA	uc001khw.1	-						CPEB3_uc001khu.1_Intron|CPEB3_uc001khv.1_Intron|CPEB3_uc010qnn.1_Intron	NM_014912	NP_055727			cytoplasmic polyadenylation element binding								nucleotide binding|RNA binding				0		Colorectal(252;0.0869)																---	---	---	---
CPEB3	22849	broad.mit.edu	37	10	93904961	93904961	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93904961delA	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	94104452	94104452	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94104452delA	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	94236915	94236915	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94236915delT	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)													---	---	---	---
CEP55	55165	broad.mit.edu	37	10	95259630	95259630	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95259630delA	uc009xug.2	+						CEP55_uc001kiq.3_Intron	NM_001127182	NP_001120654			centrosomal protein 55kDa						cell division|mitosis	centriole|cleavage furrow|midbody					0		Colorectal(252;0.207)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	95565211	95565212	+	IGR	INS	-	TT	TT	rs112283103	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95565211_95565212insTT								LGI1 (7289 upstream) : TMEM20 (88518 downstream)																																			---	---	---	---
NOC3L	64318	broad.mit.edu	37	10	96094287	96094288	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96094287_96094288delAA	uc001kjq.1	-							NM_022451	NP_071896			nucleolar complex associated 3 homolog							nuclear speck|nucleolus	binding			ovary(1)	1		Colorectal(252;0.0897)																---	---	---	---
NOC3L	64318	broad.mit.edu	37	10	96119208	96119208	+	Intron	DEL	A	-	-	rs76529903		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96119208delA	uc001kjq.1	-						NOC3L_uc009xuk.1_Intron	NM_022451	NP_071896			nucleolar complex associated 3 homolog							nuclear speck|nucleolus	binding			ovary(1)	1		Colorectal(252;0.0897)																---	---	---	---
HELLS	3070	broad.mit.edu	37	10	96313731	96313731	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96313731delT	uc001kjt.2	+						HELLS_uc001kjs.2_Intron|HELLS_uc009xul.2_Intron|HELLS_uc009xum.2_Intron|HELLS_uc009xun.2_Intron|HELLS_uc009xuo.2_Intron|HELLS_uc001kju.2_Intron|HELLS_uc009xup.2_Intron|HELLS_uc009xuq.2_Intron|HELLS_uc009xur.2_Intron	NM_018063	NP_060533			helicase, lymphoid-specific						cell division|centromeric heterochromatin formation|lymphocyte proliferation|maintenance of DNA methylation|methylation-dependent chromatin silencing|mitosis|transcription, DNA-dependent	centromeric heterochromatin|nucleus	ATP binding|DNA binding|helicase activity			ovary(1)|kidney(1)	2		Colorectal(252;0.0429)		all cancers(201;2.13e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	96932999	96932999	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96932999delT								CYP2C8 (103745 upstream) : C10orf129 (20958 downstream)																																			---	---	---	---
SORBS1	10580	broad.mit.edu	37	10	97146399	97146399	+	Intron	DEL	A	-	-	rs137966891		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97146399delA	uc001kkp.2	-						SORBS1_uc001kkk.2_5'Flank|SORBS1_uc001kkl.2_Intron|SORBS1_uc001kkn.2_Intron|SORBS1_uc001kkm.2_Intron|SORBS1_uc001kko.2_Intron|SORBS1_uc001kkq.2_Intron|SORBS1_uc001kkr.2_Intron|SORBS1_uc001kks.2_Intron|SORBS1_uc001kkt.2_Intron|SORBS1_uc001kku.2_Intron|SORBS1_uc001kkv.2_Intron|SORBS1_uc001kkw.2_Intron|SORBS1_uc010qoe.1_Intron|SORBS1_uc010qof.1_Intron	NM_001034954	NP_001030126			sorbin and SH3 domain containing 1 isoform 3						focal adhesion assembly|glucose transport|insulin receptor signaling pathway|muscle contraction|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|stress fiber assembly	centrosome|cytosol|focal adhesion|membrane raft|nucleus|stress fiber|zonula adherens	actin binding|insulin receptor binding|SH3/SH2 adaptor activity			breast(1)	1		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)														---	---	---	---
SORBS1	10580	broad.mit.edu	37	10	97167979	97167981	+	Intron	DEL	CTC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97167979_97167981delCTC	uc001kkp.2	-						SORBS1_uc001kkl.2_Intron|SORBS1_uc001kkn.2_Intron|SORBS1_uc001kkm.2_Intron|SORBS1_uc001kko.2_Intron|SORBS1_uc001kkq.2_Intron|SORBS1_uc001kkr.2_Intron|SORBS1_uc001kks.2_Intron|SORBS1_uc001kkt.2_Intron|SORBS1_uc001kku.2_Intron|SORBS1_uc001kkv.2_Intron|SORBS1_uc001kkw.2_Intron|SORBS1_uc010qoe.1_Intron|SORBS1_uc010qof.1_Intron	NM_001034954	NP_001030126			sorbin and SH3 domain containing 1 isoform 3						focal adhesion assembly|glucose transport|insulin receptor signaling pathway|muscle contraction|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|stress fiber assembly	centrosome|cytosol|focal adhesion|membrane raft|nucleus|stress fiber|zonula adherens	actin binding|insulin receptor binding|SH3/SH2 adaptor activity			breast(1)	1		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)														---	---	---	---
ALDH18A1	5832	broad.mit.edu	37	10	97406814	97406814	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97406814delT	uc001kkz.2	-						ALDH18A1_uc001kky.2_Intron|ALDH18A1_uc010qog.1_Intron|ALDH18A1_uc010qoh.1_Intron	NM_002860	NP_002851			pyrroline-5-carboxylate synthetase isoform 1						proline biosynthetic process	mitochondrial inner membrane	ATP binding|glutamate 5-kinase activity|glutamate-5-semialdehyde dehydrogenase activity			pancreas(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0402)		Epithelial(162;9.1e-07)|all cancers(201;2.55e-05)	L-Glutamic Acid(DB00142)													---	---	---	---
ENTPD1	953	broad.mit.edu	37	10	97592148	97592148	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97592148delA	uc001klh.3	+						ENTPD1_uc001kle.1_Intron|ENTPD1_uc001kli.3_Intron|uc001klg.1_Intron|ENTPD1_uc010qoj.1_Intron|ENTPD1_uc010qok.1_Intron|ENTPD1_uc010qol.1_Intron|ENTPD1_uc010qom.1_Intron|ENTPD1_uc010qon.1_Intron|ENTPD1_uc009xva.2_Intron|ENTPD1_uc009xuz.2_Intron	NM_001776	NP_001767			ectonucleoside triphosphate diphosphohydrolase 1						cell adhesion	integral to plasma membrane	ATP binding			ovary(3)	3		Colorectal(252;0.0821)		Epithelial(162;1.31e-07)|all cancers(201;5.33e-06)														---	---	---	---
ENTPD1	953	broad.mit.edu	37	10	97634898	97634898	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97634898delA	uc001klh.3	+	10					ENTPD1_uc001kli.3_3'UTR|uc001klg.1_Intron|ENTPD1_uc010qoj.1_3'UTR|ENTPD1_uc010qok.1_3'UTR|ENTPD1_uc010qol.1_3'UTR|ENTPD1_uc010qom.1_3'UTR|ENTPD1_uc010qon.1_3'UTR|ENTPD1_uc009xva.2_3'UTR|ENTPD1_uc009xuz.2_RNA	NM_001776	NP_001767			ectonucleoside triphosphate diphosphohydrolase 1						cell adhesion	integral to plasma membrane	ATP binding			ovary(3)	3		Colorectal(252;0.0821)		Epithelial(162;1.31e-07)|all cancers(201;5.33e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	97729517	97729517	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97729517delA	uc001klg.1	-						uc001klj.1_Intron					Homo sapiens cDNA FLJ34077 fis, clone FCBBF3003481, weakly similar to ZINC FINGER PROTEIN 195.																														---	---	---	---
TLL2	7093	broad.mit.edu	37	10	98198914	98198916	+	Intron	DEL	GTG	-	-	rs112897982		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98198914_98198916delGTG	uc001kml.1	-						TLL2_uc009xvf.1_Intron	NM_012465	NP_036597			tolloid-like 2 precursor						cell differentiation|multicellular organismal development|proteolysis	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)														---	---	---	---
ARHGAP19	84986	broad.mit.edu	37	10	98997629	98997629	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98997629delA	uc001knb.2	-						ARHGAP19_uc001kmy.2_Intron|ARHGAP19_uc001kna.2_Intron|ARHGAP19_uc009xvi.2_Intron|ARHGAP19_uc009xvj.2_Intron|ARHGAP19_uc009xvk.2_Intron	NM_032900	NP_116289			Rho GTPase activating protein 19						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|nucleus	GTPase activator activity				0		Colorectal(252;0.0854)		Epithelial(162;7.65e-09)|all cancers(201;4.49e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	99056628	99056629	+	IGR	DEL	AG	-	-	rs58803035		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99056628_99056629delAG								ARHGAP19 (4215 upstream) : FRAT1 (22393 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	99105955	99105955	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99105955delA								FRAT2 (11497 upstream) : RRP12 (10504 downstream)																																			---	---	---	---
ANKRD2	26287	broad.mit.edu	37	10	99339916	99339917	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99339916_99339917insA	uc001knw.2	+						ANKRD2_uc009xvu.2_Intron	NM_020349	NP_065082			ankyrin repeat domain 2 isoform a						muscle contraction|muscle organ development		structural constituent of muscle				0		all_hematologic(284;1.95e-06)|Colorectal(252;0.0163)		Epithelial(162;1.18e-94)|all cancers(201;9.31e-86)|BRCA - Breast invasive adenocarcinoma(275;0.0233)|STAD - Stomach adenocarcinoma(243;0.181)|KIRC - Kidney renal clear cell carcinoma(50;0.206)|Kidney(138;0.241)														---	---	---	---
PI4K2A	55361	broad.mit.edu	37	10	99361194	99361195	+	Intron	INS	-	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99361194_99361195insG	uc010qoy.1	+						DHDPSL_uc001kny.2_Intron|DHDPSL_uc001knz.2_Intron	NM_018425	NP_060895			phosphatidylinositol 4-kinase type 2 alpha						phosphatidylinositol biosynthetic process	cytoplasm|integral to plasma membrane|membrane raft	1-phosphatidylinositol 4-kinase activity|ATP binding|magnesium ion binding			lung(1)|skin(1)	2		Colorectal(252;0.162)		Epithelial(162;1.24e-10)|all cancers(201;1.2e-08)														---	---	---	---
PI4K2A	55361	broad.mit.edu	37	10	99431216	99431216	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99431216delA	uc001kog.1	+						PI4K2A_uc010qoy.1_Intron|PI4K2A_uc009xvw.1_Intron	NM_018425	NP_060895			phosphatidylinositol 4-kinase type 2 alpha						phosphatidylinositol biosynthetic process	cytoplasm|integral to plasma membrane|membrane raft	1-phosphatidylinositol 4-kinase activity|ATP binding|magnesium ion binding			lung(1)|skin(1)	2		Colorectal(252;0.162)		Epithelial(162;1.24e-10)|all cancers(201;1.2e-08)														---	---	---	---
PYROXD2	84795	broad.mit.edu	37	10	100167326	100167326	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100167326delG	uc001kpc.2	-						PYROXD2_uc001kpb.2_Intron|PYROXD2_uc001kpd.2_Intron|PYROXD2_uc010qpe.1_Intron	NM_032709	NP_116098			pyridine nucleotide-disulphide oxidoreductase								oxidoreductase activity			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	101205266	101205266	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101205266delT								GOT1 (14736 upstream) : NKX2-3 (87424 downstream)																																			---	---	---	---
NKX2-3	159296	broad.mit.edu	37	10	101293574	101293574	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101293574delC	uc009xwj.2	+						uc001kps.1_5'Flank	NM_145285	NP_660328			NK2 transcription factor related, locus 3							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;4.72e-10)|all cancers(201;3.45e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	101297894	101297894	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101297894delA								NKX2-3 (1616 upstream) : SLC25A28 (72381 downstream)																																			---	---	---	---
SEC31B	25956	broad.mit.edu	37	10	102253787	102253787	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102253787delA	uc001krc.1	-						SEC31B_uc010qpo.1_Intron|SEC31B_uc001krd.1_Intron|SEC31B_uc001krf.1_Intron|SEC31B_uc001kre.1_Intron	NM_015490	NP_056305			SEC31 homolog B						protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane				ovary(1)	1		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)														---	---	---	---
SEC31B	25956	broad.mit.edu	37	10	102264773	102264773	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102264773delT	uc001krc.1	-						SEC31B_uc010qpo.1_Intron|SEC31B_uc001krd.1_Intron|SEC31B_uc001krf.1_Intron|SEC31B_uc001kre.1_Intron|SEC31B_uc001krg.1_Intron	NM_015490	NP_056305			SEC31 homolog B						protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane				ovary(1)	1		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)														---	---	---	---
HIF1AN	55662	broad.mit.edu	37	10	102310614	102310614	+	3'UTR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102310614delC	uc001krj.3	+	8						NM_017902	NP_060372			hypoxia-inducible factor 1, alpha subunit						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|protein binding				0		Colorectal(252;0.234)		Epithelial(162;6.75e-10)|all cancers(201;4.88e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	102931554	102931554	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102931554delT								TLX1 (34009 upstream) : LBX1 (55180 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	102984993	102984993	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102984993delT								TLX1 (87448 upstream) : LBX1 (1741 downstream)																																			---	---	---	---
LBX1	10660	broad.mit.edu	37	10	102991466	102991467	+	5'Flank	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102991466_102991467delAG	uc001ksx.2	-						uc010qpy.1_Intron	NM_006562	NP_006553			ladybird homeobox 1						muscle organ development		sequence-specific DNA binding				0		Colorectal(252;0.234)		Epithelial(162;3.22e-09)|all cancers(201;1.79e-07)														---	---	---	---
BTRC	8945	broad.mit.edu	37	10	103228203	103228203	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103228203delA	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)														---	---	---	---
SUFU	51684	broad.mit.edu	37	10	104367988	104367989	+	Intron	DEL	AA	-	-	rs76665733		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104367988_104367989delAA	uc001kvy.1	+						SUFU_uc001kvw.1_Intron|SUFU_uc001kvx.2_Intron|SUFU_uc009xxe.1_Intron|SUFU_uc009xxf.1_Intron	NM_016169	NP_057253			suppressor of fused						negative regulation of transcription from RNA polymerase II promoter|proteolysis|skeletal system development	cytoplasm|nucleus	identical protein binding|protein binding|signal transducer activity|transcription corepressor activity|transcription factor binding			central_nervous_system(4)|skin(2)|breast(1)	7		Colorectal(252;0.207)		Epithelial(162;1.36e-08)|all cancers(201;3.81e-07)|BRCA - Breast invasive adenocarcinoma(275;0.242)				D|F|S		medulloblastoma	medulloblastoma			Medulloblastoma_associated_with_Germline_SUFU_Mutation				---	---	---	---
AS3MT	57412	broad.mit.edu	37	10	104630328	104630328	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104630328delA	uc001kwk.2	+						AS3MT_uc001kwj.2_Intron|AS3MT_uc009xxh.2_Intron	NM_020682	NP_065733			arsenic (+3 oxidation state) methyltransferase						arsonoacetate metabolic process|toxin metabolic process	cytosol	arsenite methyltransferase activity|methylarsonite methyltransferase activity				0		Colorectal(252;0.122)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;5.87e-09)|all cancers(201;1.58e-07)|BRCA - Breast invasive adenocarcinoma(275;0.223)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	105682607	105682608	+	IGR	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105682607_105682608delCT								OBFC1 (4562 upstream) : SLK (44862 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	106237454	106237454	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106237454delT								CCDC147 (22615 upstream) : SORCS3 (163405 downstream)																																			---	---	---	---
SORCS3	22986	broad.mit.edu	37	10	106681243	106681244	+	Intron	INS	-	TC	TC	rs71881115		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106681243_106681244insTC	uc001kyi.1	+							NM_014978	NP_055793			VPS10 domain receptor protein SORCS 3 precursor							integral to membrane	neuropeptide receptor activity			ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)														---	---	---	---
SORCS3	22986	broad.mit.edu	37	10	106730295	106730295	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106730295delT	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)														---	---	---	---
SORCS1	114815	broad.mit.edu	37	10	108346170	108346170	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108346170delT	uc001kym.2	-						SORCS1_uc001kyl.2_Intron|SORCS1_uc009xxs.2_Intron|SORCS1_uc001kyn.1_Intron|SORCS1_uc001kyo.2_Intron	NM_052918	NP_443150			SORCS receptor 1 isoform a							integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	109111048	109111048	+	IGR	DEL	A	-	-	rs141189228		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:109111048delA								SORCS1 (186756 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	110657046	110657047	+	IGR	DEL	TT	-	-	rs149316011		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:110657046_110657047delTT								None (None upstream) : XPNPEP1 (967477 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	110726174	110726175	+	IGR	DEL	AA	-	-	rs71678459		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:110726174_110726175delAA								None (None upstream) : XPNPEP1 (898349 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	110732491	110732494	+	IGR	DEL	AGAG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:110732491_110732494delAGAG								None (None upstream) : XPNPEP1 (892030 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	110749262	110749262	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:110749262delT								None (None upstream) : XPNPEP1 (875262 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	110901817	110901817	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:110901817delA								None (None upstream) : XPNPEP1 (722707 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	111494803	111494804	+	IGR	DEL	AA	-	-	rs113597145		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111494803_111494804delAA								None (None upstream) : XPNPEP1 (129720 downstream)																																			---	---	---	---
SMNDC1	10285	broad.mit.edu	37	10	112055217	112055217	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112055217delA	uc001kzc.3	-						SMNDC1_uc001kzb.2_Intron	NM_005871	NP_005862			survival motor neuron domain containing 1						apoptosis|induction of apoptosis|mRNA processing|RNA splicing, via transesterification reactions	Cajal body|cytoplasm|nuclear speck|spliceosomal complex	protein binding|RNA binding			skin(1)	1		Breast(234;0.174)		Epithelial(162;6.86e-05)|all cancers(201;0.00149)|BRCA - Breast invasive adenocarcinoma(275;0.119)														---	---	---	---
RBM20	282996	broad.mit.edu	37	10	112461006	112461006	+	Intron	DEL	T	-	-	rs79352713		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112461006delT	uc001kzf.2	+							NM_001134363	NP_001127835			RNA binding motif protein 20							nucleus	nucleotide binding|RNA binding|zinc ion binding				0																		---	---	---	---
SHOC2	8036	broad.mit.edu	37	10	112681536	112681537	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112681536_112681537insT	uc001kzl.3	+						SHOC2_uc009xxx.2_Intron|SHOC2_uc010qrg.1_Intron|NCRNA00081_uc009xxw.2_5'Flank|NCRNA00081_uc001kzi.3_5'Flank|NCRNA00081_uc001kzj.3_5'Flank|NCRNA00081_uc001kzk.3_5'Flank|NCRNA00081_uc010qrf.1_5'Flank	NM_007373	NP_031399			soc-2 suppressor of clear homolog						fibroblast growth factor receptor signaling pathway|positive regulation of Ras protein signal transduction|Ras protein signal transduction	nucleus|protein phosphatase type 1 complex	protein phosphatase binding|protein phosphatase regulator activity			ovary(1)|skin(1)	2				Epithelial(162;0.000796)|all cancers(201;0.011)|BRCA - Breast invasive adenocarcinoma(275;0.126)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	113214311	113214311	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113214311delG								ADRA2A (373651 upstream) : GPAM (695311 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	113667051	113667052	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113667051_113667052insA								ADRA2A (826391 upstream) : GPAM (242570 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	113845760	113845760	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113845760delA								None (None upstream) : GPAM (63862 downstream)																																			---	---	---	---
VTI1A	143187	broad.mit.edu	37	10	114332283	114332283	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114332283delA	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	115269329	115269329	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115269329delA								TCF7L2 (341895 upstream) : HABP2 (43449 downstream)																																			---	---	---	---
NHLRC2	374354	broad.mit.edu	37	10	115637007	115637009	+	Intron	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115637007_115637009delTTT	uc001lax.1	+							NM_198514	NP_940916			NHL repeat containing 2						cell redox homeostasis					ovary(1)	1				Epithelial(162;0.017)|all cancers(201;0.0187)														---	---	---	---
C10orf118	55088	broad.mit.edu	37	10	115887224	115887224	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115887224delT	uc001lbb.1	-	14	3041	c.2389delA	c.(2389-2391)ACAfs	p.T797fs	C10orf118_uc009xyd.1_Frame_Shift_Del_p.T395fs|C10orf118_uc001lbc.1_Frame_Shift_Del_p.T797fs|C10orf118_uc009xye.1_Intron	NM_018017	NP_060487	Q7Z3E2	CJ118_HUMAN	CTCL tumor antigen L14-2	797	Potential.									ovary(2)	2		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0161)|all cancers(201;0.0397)														---	---	---	---
ATRNL1	26033	broad.mit.edu	37	10	116887545	116887545	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116887545delT	uc001lcg.2	+						ATRNL1_uc001lce.2_Intron|ATRNL1_uc001lcf.2_Intron|ATRNL1_uc009xyq.2_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	117090358	117090358	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117090358delT	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	117403795	117403795	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117403795delT	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	118172810	118172810	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118172810delT								C10orf96 (33270 upstream) : PNLIPRP3 (14614 downstream)																																			---	---	---	---
PNLIP	5406	broad.mit.edu	37	10	118313457	118313458	+	Intron	DEL	AA	-	-	rs72574709		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118313457_118313458delAA	uc001lcm.2	+							NM_000936	NP_000927			pancreatic lipase precursor						lipid catabolic process|retinoid metabolic process|steroid metabolic process	extracellular region	retinyl-palmitate esterase activity|triglyceride lipase activity			ovary(1)|central_nervous_system(1)|skin(1)	3				all cancers(201;0.0131)	Bentiromide(DB00522)|Orlistat(DB01083)													---	---	---	---
HSPA12A	259217	broad.mit.edu	37	10	118451344	118451344	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118451344delC	uc001lct.2	-						HSPA12A_uc001lcu.2_Intron	NM_025015	NP_079291			heat shock 70kDa protein 12A								ATP binding			ovary(1)	1				all cancers(201;0.0158)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	118906950	118906951	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118906950_118906951delAA								VAX1 (9138 upstream) : KCNK18 (50049 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	119450791	119450791	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119450791delT								EMX2 (141735 upstream) : RAB11FIP2 (313638 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	119748272	119748273	+	IGR	INS	-	TGTG	TGTG	rs145060173	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119748272_119748273insTGTG								EMX2 (439216 upstream) : RAB11FIP2 (16156 downstream)																																			---	---	---	---
CASC2	255082	broad.mit.edu	37	10	119967766	119967766	+	RNA	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119967766delA	uc001ldm.3	+	5		c.1374delA			CASC2_uc009xzc.2_RNA	NR_026939				Homo sapiens mRNA for IGM1 protein.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	120119071	120119072	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120119071_120119072delTG								C10orf84 (17232 upstream) : PRLHR (233844 downstream)																																			---	---	---	---
C10orf46	143384	broad.mit.edu	37	10	120487661	120487661	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120487661delA	uc001lds.1	-						C10orf46_uc010qst.1_Intron	NM_153810	NP_722517			chromosome 10 open reading frame 46						ubiquitin-dependent protein catabolic process	cullin-RING ubiquitin ligase complex	ubiquitin protein ligase binding				0		Lung NSC(174;0.142)|all_lung(145;0.175)		all cancers(201;0.0131)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	120695301	120695301	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120695301delA								C10orf46 (180543 upstream) : NANOS1 (93927 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	120780136	120780137	+	IGR	INS	-	ACAC	ACAC	rs146083832	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120780136_120780137insACAC								C10orf46 (265378 upstream) : NANOS1 (9091 downstream)																																			---	---	---	---
EIF3A	8661	broad.mit.edu	37	10	120795796	120795796	+	Intron	DEL	A	-	-	rs75955170		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120795796delA	uc001ldu.2	-						EIF3A_uc010qsu.1_Intron	NM_003750	NP_003741			eukaryotic translation initiation factor 3,						formation of translation initiation complex	cytosol|eukaryotic translation initiation factor 3 complex	protein binding|structural molecule activity|translation initiation factor activity				0		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0236)														---	---	---	---
SEC23IP	11196	broad.mit.edu	37	10	121683066	121683068	+	Intron	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121683066_121683068delTTT	uc001leu.1	+						SEC23IP_uc010qtc.1_Intron|SEC23IP_uc009xzk.1_Intron	NM_007190	NP_009121			Sec23-interacting protein p125						Golgi organization|intracellular protein transport	endoplasmic reticulum|ER to Golgi transport vesicle membrane|ER-Golgi intermediate compartment	metal ion binding			ovary(3)	3		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	122178710	122178710	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122178710delA								SEC23IP (477465 upstream) : PPAPDC1A (37756 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	123123448	123123448	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123123448delT								WDR11 (454413 upstream) : FGFR2 (114397 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	123182137	123182138	+	IGR	DEL	TG	-	-	rs72426107		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123182137_123182138delTG								WDR11 (513102 upstream) : FGFR2 (55707 downstream)																																			---	---	---	---
TACC2	10579	broad.mit.edu	37	10	123947976	123947976	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123947976delT	uc001lfv.2	+						TACC2_uc001lfw.2_Intron|TACC2_uc009xzx.2_Intron|TACC2_uc010qtv.1_Intron|TACC2_uc001lfx.2_Intron|TACC2_uc001lfy.2_Intron|TACC2_uc001lfz.2_Intron|TACC2_uc001lga.2_Intron|TACC2_uc009xzy.2_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	124485373	124485376	+	IGR	DEL	CACA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124485373_124485376delCACA								C10orf120 (26035 upstream) : FLJ46361 (30834 downstream)																																			---	---	---	---
C10orf88	80007	broad.mit.edu	37	10	124711352	124711352	+	Intron	DEL	A	-	-	rs75488600		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124711352delA	uc001lgw.2	-						C10orf88_uc001lgx.2_Intron	NM_024942	NP_079218			hypothetical protein LOC80007												0		all_neural(114;0.0765)|Lung NSC(174;0.163)|all_lung(145;0.205)		Colorectal(40;0.0686)|COAD - Colon adenocarcinoma(40;0.0735)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	124928373	124928374	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124928373_124928374delTT								BUB3 (3487 upstream) : GPR26 (497497 downstream)																																			---	---	---	---
CPXM2	119587	broad.mit.edu	37	10	125659567	125659567	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125659567delT	uc001lhj.2	-											Homo sapiens cDNA FLJ56000 complete cds, highly similar to Carboxypeptidase-like protein X2 precursor.						cell adhesion|proteolysis	extracellular space	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)														---	---	---	---
CHST15	51363	broad.mit.edu	37	10	125793335	125793335	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125793335delC	uc001lhl.2	-						CHST15_uc001lhm.2_Intron|CHST15_uc001lhn.2_Intron|CHST15_uc010que.1_Intron|CHST15_uc001lho.2_Intron	NM_015892	NP_056976			B cell RAG associated protein						hexose biosynthetic process	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity			ovary(1)	1																		---	---	---	---
LHPP	64077	broad.mit.edu	37	10	126198133	126198133	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126198133delT	uc001lhs.1	+						LHPP_uc001lht.1_Intron|LHPP_uc009yai.1_Intron	NM_022126	NP_071409			phospholysine phosphohistidine inorganic						protein dephosphorylation	cytosol|nucleus	inorganic diphosphatase activity|magnesium ion binding|phosphohistidine phosphatase activity|protein homodimerization activity				0		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.163)|Colorectal(40;0.187)														---	---	---	---
LHPP	64077	broad.mit.edu	37	10	126276868	126276868	+	Intron	DEL	T	-	-	rs72152076		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126276868delT	uc001lhs.1	+						LHPP_uc001lht.1_Intron|LHPP_uc009yai.1_Intron	NM_022126	NP_071409			phospholysine phosphohistidine inorganic						protein dephosphorylation	cytosol|nucleus	inorganic diphosphatase activity|magnesium ion binding|phosphohistidine phosphatase activity|protein homodimerization activity				0		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.163)|Colorectal(40;0.187)														---	---	---	---
FAM53B	9679	broad.mit.edu	37	10	126329507	126329507	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126329507delC	uc001lhv.1	-						FAM53B_uc001lhu.1_Intron	NM_014661	NP_055476			hypothetical protein LOC9679											ovary(1)|pancreas(1)	2		all_lung(145;0.0191)|Lung NSC(174;0.0301)|Colorectal(57;0.106)|all_neural(114;0.117)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.15)														---	---	---	---
FAM175B	23172	broad.mit.edu	37	10	126495202	126495202	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126495202delT	uc001lib.3	+							NM_032182	NP_115558			hypothetical protein LOC23172							BRISC complex	polyubiquitin binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	127402506	127402506	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127402506delT	uc001lim.1	-											Homo sapiens cDNA FLJ37035 fis, clone BRACE2011545.																														---	---	---	---
DHX32	55760	broad.mit.edu	37	10	127579684	127579685	+	Intron	INS	-	T	T	rs140105042		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127579684_127579685insT	uc001ljg.1	-							NM_018180	NP_060650			DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32							mitochondrion|nucleus	ATP binding|helicase activity			breast(2)|ovary(1)|lung(1)	4		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)																---	---	---	---
ADAM12	8038	broad.mit.edu	37	10	128030405	128030405	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128030405delT	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)														---	---	---	---
C10orf90	118611	broad.mit.edu	37	10	128200879	128200880	+	Intron	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128200879_128200880delTG	uc001ljq.2	-						C10orf90_uc010qum.1_Intron|C10orf90_uc009yao.2_Intron|C10orf90_uc001ljs.1_Intron	NM_001004298	NP_001004298			hypothetical protein LOC118611											ovary(1)|skin(1)	2		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)														---	---	---	---
DOCK1	1793	broad.mit.edu	37	10	128869281	128869281	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128869281delT	uc001ljt.2	+						DOCK1_uc010qun.1_Intron	NM_001380	NP_001371			dedicator of cytokinesis 1						apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	131045772	131045772	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131045772delA								None (None upstream) : MGMT (219682 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	131594484	131594484	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131594484delT								MGMT (28701 upstream) : EBF3 (39063 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	131896017	131896018	+	Intron	INS	-	T	T	rs142306547	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131896017_131896018insT	uc010qus.1	-											Homo sapiens cDNA FLJ36799 fis, clone ADRGL2007357.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	132439570	132439570	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132439570delT								GLRX3 (456786 upstream) : TCERG1L (451086 downstream)																																			---	---	---	---
TCERG1L	256536	broad.mit.edu	37	10	133090045	133090045	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133090045delA	uc001lkp.2	-							NM_174937	NP_777597			transcription elongation regulator 1-like											large_intestine(2)|ovary(2)	4		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	133470945	133470945	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133470945delG								TCERG1L (360961 upstream) : PPP2R2D (277015 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	134628164	134628164	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134628164delC	uc010qux.1	-							NM_017609	NP_060079			Homo sapiens cDNA, FLJ17989.																														---	---	---	---
TUBGCP2	10844	broad.mit.edu	37	10	135113670	135113670	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135113670delA	uc001lmg.1	-						TUBGCP2_uc010qvc.1_Intron|TUBGCP2_uc009ybk.1_Intron|TUBGCP2_uc010qvd.1_Intron|TUBGCP2_uc001lmh.1_Intron	NM_006659	NP_006650			tubulin, gamma complex associated protein 2						G2/M transition of mitotic cell cycle|microtubule nucleation|protein complex assembly	centrosome|cytoplasmic microtubule|cytosol|spindle pole	protein binding				0		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	135474720	135474721	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135474720_135474721delTC								FRG2B (34421 upstream) : LOC653544 (15558 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	135500236	135500237	+	IGR	INS	-	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135500236_135500237insC								LOC653544 (5043 upstream) : None (None downstream)																																			---	---	---	---
PTDSS2	81490	broad.mit.edu	37	11	478452	478452	+	Intron	DEL	A	-	-	rs77505779		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:478452delA	uc001lpj.2	+						PTDSS2_uc009ybv.1_Intron	NM_030783	NP_110410			phosphatidylserine synthase 2							integral to membrane					0		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;2.76e-26)|Epithelial(43;2.56e-25)|OV - Ovarian serous cystadenocarcinoma(40;7.54e-20)|BRCA - Breast invasive adenocarcinoma(625;8.76e-05)|Lung(200;0.0407)|LUSC - Lung squamous cell carcinoma(625;0.0735)	Phosphatidylserine(DB00144)													---	---	---	---
PHRF1	57661	broad.mit.edu	37	11	578859	578859	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:578859delT	uc001lqe.2	+						LOC143666_uc010qwb.1_5'Flank|PHRF1_uc010qwc.1_Intron|PHRF1_uc010qwd.1_Intron|PHRF1_uc010qwe.1_Intron	NM_020901	NP_065952			PHD and ring finger domains 1								RNA polymerase binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	1067339	1067340	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1067339_1067340delTT								MUC6 (30633 upstream) : MUC2 (7535 downstream)																																			---	---	---	---
MUC5B	727897	broad.mit.edu	37	11	1141907	1141908	+	5'Flank	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1141907_1141908delGT	uc009ycr.1	+							NM_017511	NP_059981			SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;						cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)														---	---	---	---
BRSK2	9024	broad.mit.edu	37	11	1440899	1440899	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1440899delG	uc001lti.2	+						BRSK2_uc009ycv.1_Intron|BRSK2_uc001lth.1_Intron|BRSK2_uc001ltj.2_Intron|BRSK2_uc001ltk.2_Intron|BRSK2_uc001ltl.2_Intron|BRSK2_uc001ltm.2_Intron	NM_003957	NP_003948			BR serine/threonine kinase 2						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)														---	---	---	---
BRSK2	9024	broad.mit.edu	37	11	1468404	1468404	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1468404delG	uc001lti.2	+						BRSK2_uc009ycv.1_Intron|BRSK2_uc001lth.1_Intron|BRSK2_uc001ltj.2_Intron|BRSK2_uc001ltk.2_Intron|BRSK2_uc001ltl.2_Intron|BRSK2_uc001ltm.2_Intron|BRSK2_uc001ltn.2_Intron|BRSK2_uc010qwx.1_Intron	NM_003957	NP_003948			BR serine/threonine kinase 2						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)														---	---	---	---
TNNI2	7136	broad.mit.edu	37	11	1861691	1861691	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1861691delG	uc010qxe.1	+						TNNI2_uc010qxc.1_Intron|TNNI2_uc010qxd.1_Intron	NM_001145841	NP_001139313			fast-twitch skeletal muscle troponin I isoform						muscle filament sliding|positive regulation of transcription, DNA-dependent|skeletal muscle contraction	cytosol|nucleus|troponin complex	actin binding|troponin T binding				0		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00136)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	2139807	2139807	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2139807delA								H19 (120742 upstream) : IGF2 (10541 downstream)																																			---	---	---	---
KCNQ1	3784	broad.mit.edu	37	11	2648965	2648966	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2648965_2648966delAC	uc001lwn.2	+						KCNQ1_uc009ydp.1_Intron|KCNQ1_uc001lwo.2_Intron	NM_000218	NP_000209			potassium voltage-gated channel, KQT-like						blood circulation|membrane depolarization|muscle contraction|sensory perception of sound		delayed rectifier potassium channel activity|protein binding			ovary(1)	1		all_epithelial(84;3.26e-05)|Breast(177;0.001)|Medulloblastoma(188;0.00111)|Ovarian(85;0.00158)|all_neural(188;0.00725)|all_lung(207;0.11)|Lung NSC(207;0.159)		BRCA - Breast invasive adenocarcinoma(625;0.00251)|Lung(200;0.131)	Bepridil(DB01244)|Indapamide(DB00808)													---	---	---	---
CARS	833	broad.mit.edu	37	11	3026849	3026850	+	Intron	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3026849_3026850delTG	uc001lxh.2	-						CARS_uc009ydu.2_Intron|CARS_uc001lxe.2_Intron|CARS_uc001lxf.2_Intron|CARS_uc001lxg.2_Intron|CARS_uc010qxo.1_Intron|CARS_uc010qxp.1_Intron	NM_001751	NP_001742			cysteinyl-tRNA synthetase isoform b						cysteinyl-tRNA aminoacylation	cytoplasm|cytosol	ATP binding|cysteine-tRNA ligase activity|metal ion binding|protein homodimerization activity|protein homodimerization activity|tRNA binding|tRNA binding		CARS/ALK(5)	soft_tissue(5)|ovary(2)	7		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00317)|LUSC - Lung squamous cell carcinoma(625;0.218)	L-Cysteine(DB00151)			T	ALK	ALCL								---	---	---	---
Unknown	0	broad.mit.edu	37	11	3607787	3607788	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3607787_3607788delAA								LOC650368 (177409 upstream) : TRPC2 (30674 downstream)																																			---	---	---	---
NUP98	4928	broad.mit.edu	37	11	3727549	3727549	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3727549delT	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								---	---	---	---
NUP98	4928	broad.mit.edu	37	11	3756559	3756560	+	Intron	DEL	TA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3756559_3756560delTA	uc001lyh.2	-						NUP98_uc001lyi.2_Intron|NUP98_uc001lyj.1_Intron|NUP98_uc001lyk.1_Intron	NM_016320	NP_057404			nucleoporin 98kD isoform 1						carbohydrate metabolic process|DNA replication|glucose transport|interspecies interaction between organisms|mitotic prometaphase|mRNA transport|nuclear pore organization|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear membrane|nucleoplasm|Nup107-160 complex	protein binding|structural constituent of nuclear pore|transporter activity			breast(4)|skin(3)|ovary(2)|central_nervous_system(1)|lung(1)|kidney(1)	12		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)				T	HOXA9|NSD1|WHSC1L1|DDX10|TOP1|HOXD13|PMX1|HOXA13|HOXD11|HOXA11|RAP1GDS1|HOXC11	AML								---	---	---	---
PGAP2	27315	broad.mit.edu	37	11	3847566	3847566	+	3'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3847566delT	uc001lys.2	+	7					PGAP2_uc001lyl.2_3'UTR|PGAP2_uc010qxw.1_3'UTR|PGAP2_uc010qxx.1_3'UTR|PGAP2_uc001lyp.3_3'UTR|PGAP2_uc010qxy.1_3'UTR|PGAP2_uc010qxz.1_3'UTR|PGAP2_uc001lyn.3_3'UTR|PGAP2_uc010qya.1_RNA|PGAP2_uc001lyr.2_3'UTR|PGAP2_uc010qyb.1_3'UTR|PGAP2_uc001lyt.2_3'UTR	NM_014489	NP_055304			FGF receptor activating protein 1 isoform 1						GPI anchor biosynthetic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	protein transporter activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	6067831	6067831	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6067831delG								OR56A1 (18897 upstream) : OR56B4 (61178 downstream)																																			---	---	---	---
PPFIBP2	8495	broad.mit.edu	37	11	7646362	7646362	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7646362delT	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	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)														---	---	---	---
TUB	7275	broad.mit.edu	37	11	8113944	8113944	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8113944delA	uc001mga.2	+						TUB_uc010rbk.1_Intron|TUB_uc001mfy.2_Intron	NM_177972	NP_813977			tubby isoform b						phagocytosis|positive regulation of phagocytosis|response to stimulus	cytoplasm|extracellular region|nucleus|plasma membrane				ovary(1)	1		all_lung(207;6.91e-20)|Lung NSC(207;3.36e-17)		Epithelial(150;1.69e-62)|BRCA - Breast invasive adenocarcinoma(625;8.54e-06)|LUSC - Lung squamous cell carcinoma(625;0.000184)														---	---	---	---
RIC3	79608	broad.mit.edu	37	11	8167234	8167235	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8167234_8167235delTT	uc001mgd.2	-						RIC3_uc001mgc.2_Intron|RIC3_uc001mge.2_Intron|RIC3_uc010rbl.1_Intron|RIC3_uc010rbm.1_Intron|RIC3_uc009yfm.2_Intron|RIC3_uc009yfn.2_Intron|RIC3_uc001mgf.3_Intron	NM_024557	NP_078833			resistance to inhibitors of cholinesterase 3							endoplasmic reticulum membrane|Golgi membrane|integral to membrane				large_intestine(1)|ovary(1)|pancreas(1)	3				Epithelial(150;2.89e-07)|BRCA - Breast invasive adenocarcinoma(625;0.204)														---	---	---	---
STK33	65975	broad.mit.edu	37	11	8614169	8614169	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8614169delT	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)														---	---	---	---
ST5	6764	broad.mit.edu	37	11	8791314	8791316	+	Intron	DEL	AAG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8791314_8791316delAAG	uc001mgt.2	-						ST5_uc009yfr.2_Intron|ST5_uc001mgu.2_Intron|ST5_uc001mgv.2_Intron|ST5_uc001mgw.1_Intron	NM_213618	NP_998783			suppression of tumorigenicity 5 isoform 1						positive regulation of ERK1 and ERK2 cascade		protein binding			upper_aerodigestive_tract(1)	1				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)														---	---	---	---
SCUBE2	57758	broad.mit.edu	37	11	9102196	9102196	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9102196delA	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	9485689	9485689	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9485689delT	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	9587552	9587552	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9587552delA								ZNF143 (37482 upstream) : WEE1 (7676 downstream)																																			---	---	---	---
SWAP70	23075	broad.mit.edu	37	11	9754047	9754047	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9754047delT	uc001mhw.2	+						SWAP70_uc001mhv.2_Intron|SWAP70_uc001mhx.2_Intron	NM_015055	NP_055870			SWAP-70 protein							cytoplasm|lamellipodium|nucleus|plasma membrane	calcium ion binding|DNA binding			ovary(2)|central_nervous_system(1)	3				all cancers(16;1.21e-10)|Epithelial(150;2.81e-09)|BRCA - Breast invasive adenocarcinoma(625;0.00649)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	11107940	11107940	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11107940delG								ZBED5 (228320 upstream) : GALNTL4 (184481 downstream)																																			---	---	---	---
USP47	55031	broad.mit.edu	37	11	11970052	11970052	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11970052delA	uc001mjs.2	+	22	4058	c.3295delA	c.(3295-3297)AAAfs	p.K1099fs	USP47_uc001mjr.2_Frame_Shift_Del_p.K1031fs|USP47_uc009ygi.2_5'Flank	NM_017944	NP_060414	Q96K76	UBP47_HUMAN	ubiquitin specific protease 47	1119					base-excision repair|cellular response to UV|monoubiquitinated protein deubiquitination|negative regulation of apoptosis|negative regulation of caspase activity|negative regulation of G2/M transition of mitotic cell cycle|negative regulation of transcription, DNA-dependent|positive regulation of cell growth|response to drug|ubiquitin-dependent protein catabolic process	cytoplasm|SCF ubiquitin ligase complex	ubiquitin thiolesterase activity|ubiquitin-specific protease activity|WD40-repeat domain binding			ovary(1)|skin(1)	2				Epithelial(150;0.000339)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	12101062	12101062	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12101062delT								DKK3 (69746 upstream) : MICAL2 (14481 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	12553806	12553807	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12553806_12553807insA								PARVA (2396 upstream) : TEAD1 (142162 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	13872840	13872840	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13872840delG								FAR1 (118949 upstream) : SPON1 (111074 downstream)																																			---	---	---	---
SPON1	10418	broad.mit.edu	37	11	14101782	14101782	+	Intron	DEL	T	-	-	rs35344778		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14101782delT	uc001mle.2	+							NM_006108	NP_006099			spondin 1, extracellular matrix protein						cell adhesion	extracellular space|proteinaceous extracellular matrix	protein binding				0				Epithelial(150;0.00898)														---	---	---	---
PSMA1	5682	broad.mit.edu	37	11	14525899	14525899	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14525899delT	uc010rcp.1	-							NM_001143937				proteasome alpha 1 subunit isoform 3						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|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																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	15549637	15549637	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15549637delA								INSC (280885 upstream) : SOX6 (438359 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	15792767	15792768	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15792767_15792768delAC								INSC (524015 upstream) : SOX6 (195228 downstream)																																	OREG0020797	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SOX6	55553	broad.mit.edu	37	11	16411095	16411096	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16411095_16411096insT	uc001mme.2	-						SOX6_uc001mmd.2_Intron|SOX6_uc001mmf.2_Intron|SOX6_uc001mmg.2_Intron|SOX6_uc001mmh.1_Intron|SOX6_uc009ygs.2_Intron|SOX6_uc001mmi.3_Intron|SOX6_uc001mmj.2_Intron	NM_001145819	NP_001139291			SRY (sex determining region Y)-box 6 isoform 4						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3																		---	---	---	---
SOX6	55553	broad.mit.edu	37	11	16650167	16650168	+	Intron	INS	-	A	A	rs34931534		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16650167_16650168insA	uc001mmh.1	-											Synthetic construct DNA, clone: pF1KB8405, Homo sapiens SOX6 gene for SRY (sex determining region Y)-box 6, without stop codon, in Flexi system.						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3																		---	---	---	---
SOX6	55553	broad.mit.edu	37	11	16658629	16658629	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16658629delT	uc001mmh.1	-											Synthetic construct DNA, clone: pF1KB8405, Homo sapiens SOX6 gene for SRY (sex determining region Y)-box 6, without stop codon, in Flexi system.						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	17584254	17584254	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17584254delA								USH1C (18291 upstream) : MYOD1 (156856 downstream)																																			---	---	---	---
SAAL1	113174	broad.mit.edu	37	11	18111921	18111921	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18111921delT	uc001mnq.2	-						SAAL1_uc001mnr.2_Intron|SAAL1_uc001mns.2_Intron|SAAL1_uc009yhf.2_Intron	NM_138421	NP_612430			serum amyloid A-like 1						acute-phase response	extracellular region	binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	18664626	18664626	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18664626delG								SPTY2D1 (8606 upstream) : TMEM86A (55725 downstream)																																			---	---	---	---
PTPN5	84867	broad.mit.edu	37	11	18775119	18775121	+	Intron	DEL	CTC	-	-	rs143184509		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18775119_18775121delCTC	uc001mpd.2	-						PTPN5_uc001mpb.2_Intron|PTPN5_uc001mpc.2_Intron|PTPN5_uc001mpe.2_Intron|PTPN5_uc010rdj.1_Intron|PTPN5_uc001mpf.2_Intron|PTPN5_uc010rdk.1_Intron	NM_006906	NP_008837			protein-tyrosine-phosphatase non-receptor 5							integral to membrane	phosphotyrosine binding|protein tyrosine phosphatase activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	18899570	18899571	+	IGR	DEL	GA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18899570_18899571delGA								PTPN5 (86181 upstream) : MRGPRX1 (55790 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	18945006	18945007	+	IGR	INS	-	AA	AA	rs139908033	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18945006_18945007insAA								PTPN5 (131617 upstream) : MRGPRX1 (10354 downstream)																																			---	---	---	---
NAV2	89797	broad.mit.edu	37	11	19925956	19925956	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19925956delA	uc010rdm.1	+						NAV2_uc001mpp.2_Intron|NAV2_uc001mpr.3_Intron	NM_145117	NP_660093			neuron navigator 2 isoform 2							nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6																		---	---	---	---
HTATIP2	10553	broad.mit.edu	37	11	20404503	20404504	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20404503_20404504delTT	uc009yia.1	+						HTATIP2_uc009yib.1_Intron|HTATIP2_uc001mpx.2_Intron|HTATIP2_uc001mpz.2_Intron	NM_006410	NP_006401			HIV-1 Tat interactive protein 2, 30kDa isoform						angiogenesis|anti-apoptosis|apoptosis|cell differentiation|cellular amino acid metabolic process|induction of apoptosis|interspecies interaction between organisms|nuclear import|regulation of angiogenesis|regulation of transcription from RNA polymerase II promoter	cytoplasm|nuclear envelope	NAD binding|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor|protein binding|transcription coactivator activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	20595926	20595926	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20595926delA								PRMT3 (65049 upstream) : SLC6A5 (25020 downstream)																																			---	---	---	---
NELL1	4745	broad.mit.edu	37	11	20721589	20721590	+	Intron	INS	-	A	A	rs149053095	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20721589_20721590insA	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	20758014	20758014	+	Intron	DEL	T	-	-	rs35286627		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20758014delT	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	20948751	20948751	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20948751delT	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	21021522	21021523	+	Intron	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21021522_21021523delTG	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron	NM_006157	NP_006148			nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	22350809	22350809	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22350809delA								ANO5 (45896 upstream) : SLC17A6 (8858 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	22639844	22639844	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22639844delA								SLC17A6 (238800 upstream) : FANCF (4235 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	22883369	22883369	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22883369delA	uc001mqq.1	+											full-length cDNA clone CS0DJ011YO21 of T cells (Jurkat cell line) Cot 10-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	23469382	23469383	+	IGR	INS	-	GT	GT	rs3075934		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:23469382_23469383insGT								SVIP (618000 upstream) : None (None downstream)																																			---	---	---	---
LUZP2	338645	broad.mit.edu	37	11	24589901	24589901	+	Intron	DEL	G	-	-	rs35814960	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:24589901delG	uc001mqs.2	+						LUZP2_uc009yif.2_Intron|LUZP2_uc009yig.2_Intron	NM_001009909	NP_001009909			leucine zipper protein 2 precursor							extracellular region				ovary(1)|skin(1)	2																		---	---	---	---
SLC5A12	159963	broad.mit.edu	37	11	26720178	26720178	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26720178delT	uc001mra.2	-						SLC5A12_uc001mrb.2_Intron|SLC5A12_uc001mrc.3_Intron	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																		---	---	---	---
LGR4	55366	broad.mit.edu	37	11	27478478	27478478	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27478478delT	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	27781912	27781912	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27781912delT								BDNF (38307 upstream) : KIF18A (260251 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	27797816	27797818	+	IGR	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27797816_27797818delTTT								BDNF (54211 upstream) : KIF18A (244345 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	30312868	30312868	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30312868delA								FSHB (56045 upstream) : C11orf46 (31781 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	30762468	30762468	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30762468delA								MPPED2 (154538 upstream) : DCDC1 (202281 downstream)																																			---	---	---	---
ELP4	26610	broad.mit.edu	37	11	31561001	31561001	+	Intron	DEL	A	-	-	rs76954383		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31561001delA	uc001mtb.2	+						ELP4_uc001mta.1_Intron|ELP4_uc001mtc.2_Intron|ELP4_uc010rdz.1_Intron	NM_019040	NP_061913			elongation protein 4 homolog						histone acetylation|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|DNA-directed RNA polymerase II, holoenzyme|Elongator holoenzyme complex|transcription elongation factor complex	phosphorylase kinase regulator activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|prostate(1)	3	Lung SC(675;0.225)																	---	---	---	---
ELP4	26610	broad.mit.edu	37	11	31706984	31706984	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31706984delT	uc001mtb.2	+						ELP4_uc001mtc.2_Intron|ELP4_uc010rdz.1_Intron	NM_019040	NP_061913			elongation protein 4 homolog						histone acetylation|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|DNA-directed RNA polymerase II, holoenzyme|Elongator holoenzyme complex|transcription elongation factor complex	phosphorylase kinase regulator activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|prostate(1)	3	Lung SC(675;0.225)																	---	---	---	---
RCN1	5954	broad.mit.edu	37	11	31856399	31856400	+	Intron	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31856399_31856400delTC	uc010rea.1	+							NM_002901	NP_002892			reticulocalbin 1 precursor							endoplasmic reticulum lumen	calcium ion binding			large_intestine(1)	1	Lung SC(675;0.225)																	---	---	---	---
RCN1	5954	broad.mit.edu	37	11	31889213	31889213	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31889213delA	uc010rea.1	+							NM_002901	NP_002892			reticulocalbin 1 precursor							endoplasmic reticulum lumen	calcium ion binding			large_intestine(1)	1	Lung SC(675;0.225)																	---	---	---	---
RCN1	5954	broad.mit.edu	37	11	31980618	31980618	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31980618delT	uc010rea.1	+							NM_002901	NP_002892			reticulocalbin 1 precursor							endoplasmic reticulum lumen	calcium ion binding			large_intestine(1)	1	Lung SC(675;0.225)																	---	---	---	---
RCN1	5954	broad.mit.edu	37	11	32029408	32029408	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32029408delA	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	32153929	32153930	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32153929_32153930delAA								RCN1 (26658 upstream) : WT1 (255395 downstream)																																			---	---	---	---
CCDC73	493860	broad.mit.edu	37	11	32635951	32635951	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32635951delT	uc001mtv.2	-	16	1957	c.1913delA	c.(1912-1914)AATfs	p.N638fs		NM_001008391	NP_001008392	Q6ZRK6	CCD73_HUMAN	sarcoma antigen NY-SAR-79	638										ovary(1)|central_nervous_system(1)	2	Breast(20;0.112)																	---	---	---	---
PRRG4	79056	broad.mit.edu	37	11	32860418	32860418	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32860418delT	uc001mtx.2	+							NM_024081	NP_076986			proline rich Gla (G-carboxyglutamic acid) 4							extracellular region|Golgi apparatus|integral to membrane	calcium ion binding				0	Breast(20;0.206)																	---	---	---	---
Unknown	0	broad.mit.edu	37	11	33550881	33550881	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33550881delA								HIPK3 (174942 upstream) : C11orf41 (12996 downstream)																																			---	---	---	---
FBXO3	26273	broad.mit.edu	37	11	33775942	33775942	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33775942delT	uc001muz.2	-						FBXO3_uc010rej.1_5'Flank|FBXO3_uc001muy.2_Intron|FBXO3_uc009ykb.2_RNA|FBXO3_uc001mva.1_Intron|FBXO3_uc001mvb.1_Intron|FBXO3_uc010rek.1_Intron	NM_012175	NP_036307			F-box only protein 3 isoform 1						proteolysis	nucleus	ubiquitin-protein ligase activity			pancreas(1)	1		Lung NSC(402;0.0804)		BRCA - Breast invasive adenocarcinoma(625;0.00315)|Lung(977;0.00488)|LUSC - Lung squamous cell carcinoma(625;0.008)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	33970223	33970226	+	IGR	DEL	TCAT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33970223_33970226delTCAT								LMO2 (56387 upstream) : CAPRIN1 (103004 downstream)																																			---	---	---	---
SLC1A2	6506	broad.mit.edu	37	11	35310849	35310849	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35310849delT	uc001mwd.2	-						SLC1A2_uc001mwe.2_Intron|SLC1A2_uc010rev.1_Intron	NM_004171	NP_004162			excitatory amino acid transporter 2						D-aspartate import|L-glutamate import|synaptic transmission	integral to membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity			ovary(2)|central_nervous_system(1)	3	all_lung(20;0.211)|all_epithelial(35;0.234)	all_hematologic(20;0.109)	STAD - Stomach adenocarcinoma(6;0.00731)		L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	35617060	35617060	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35617060delT								PAMR1 (65212 upstream) : FJX1 (22675 downstream)																																			---	---	---	---
LDLRAD3	143458	broad.mit.edu	37	11	36178399	36178399	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36178399delA	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)																---	---	---	---
RAG1	5896	broad.mit.edu	37	11	36563433	36563433	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36563433delA	uc001mwt.2	+							NM_000448				recombination activating gene 1						histone monoubiquitination|immune response|pre-B cell allelic exclusion|protein autoubiquitination|T cell differentiation in thymus|V(D)J recombination	nucleus	endonuclease activity|histone binding|protein homodimerization activity|sequence-specific DNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|pancreas(1)|lung(1)|kidney(1)|skin(1)	5	all_lung(20;0.226)	all_hematologic(20;0.107)												Familial_Hemophagocytic_Lymphohistiocytosis				---	---	---	---
Unknown	0	broad.mit.edu	37	11	38375526	38375526	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:38375526delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	38748073	38748073	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:38748073delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	40105895	40105895	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40105895delT								None (None upstream) : LRRC4C (29858 downstream)																																			---	---	---	---
LRRC4C	57689	broad.mit.edu	37	11	40348870	40348871	+	Intron	INS	-	T	T	rs142386480	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40348870_40348871insT	uc001mxc.1	-						LRRC4C_uc001mxd.1_Intron	NM_020929	NP_065980			netrin-G1 ligand precursor						regulation of axonogenesis	integral to membrane	protein binding			ovary(4)|skin(3)|central_nervous_system(1)	8		all_lung(304;0.0575)|Lung NSC(402;0.138)																---	---	---	---
LRRC4C	57689	broad.mit.edu	37	11	40497891	40497892	+	Intron	INS	-	TTTT	TTTT	rs12288222		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40497891_40497892insTTTT	uc001mxc.1	-						LRRC4C_uc001mxd.1_Intron	NM_020929	NP_065980			netrin-G1 ligand precursor						regulation of axonogenesis	integral to membrane	protein binding			ovary(4)|skin(3)|central_nervous_system(1)	8		all_lung(304;0.0575)|Lung NSC(402;0.138)																---	---	---	---
LRRC4C	57689	broad.mit.edu	37	11	40584485	40584486	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40584485_40584486delTT	uc001mxc.1	-						LRRC4C_uc001mxd.1_Intron	NM_020929	NP_065980			netrin-G1 ligand precursor						regulation of axonogenesis	integral to membrane	protein binding			ovary(4)|skin(3)|central_nervous_system(1)	8		all_lung(304;0.0575)|Lung NSC(402;0.138)																---	---	---	---
LRRC4C	57689	broad.mit.edu	37	11	40614137	40614137	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40614137delT	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	42639563	42639563	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42639563delG								None (None upstream) : API5 (693942 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	43240165	43240166	+	IGR	DEL	CT	-	-	rs71997787		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43240165_43240166delCT								None (None upstream) : API5 (93339 downstream)																																			---	---	---	---
EXT2	2132	broad.mit.edu	37	11	44180672	44180673	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44180672_44180673delTT	uc001mxz.2	+						EXT2_uc010rfo.1_Intron|EXT2_uc001mxy.2_Intron|EXT2_uc009ykt.2_Intron|EXT2_uc001mya.2_Intron	NM_207122	NP_997005			exostosin 2 isoform 2						glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction	Golgi membrane|integral to membrane|intrinsic to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity			lung(2)|breast(2)|skin(1)	5								Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses				---	---	---	---
Unknown	0	broad.mit.edu	37	11	44424270	44424270	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44424270delT								ALX4 (92554 upstream) : CD82 (162871 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	44726161	44726161	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44726161delT								CD82 (84848 upstream) : TSPAN18 (155718 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	44733197	44733198	+	IGR	DEL	GA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44733197_44733198delGA								CD82 (91884 upstream) : TSPAN18 (148681 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	45349550	45349550	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45349550delA								SYT13 (41666 upstream) : CHST1 (320877 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	45577975	45577978	+	IGR	DEL	ACTA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45577975_45577978delACTA								SYT13 (270091 upstream) : CHST1 (92449 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	45800873	45800873	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45800873delT								DKFZp779M0652 (6965 upstream) : SLC35C1 (24750 downstream)																																			---	---	---	---
ARHGAP1	392	broad.mit.edu	37	11	46705194	46705195	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46705194_46705195delTT	uc001ndd.2	-							NM_004308	NP_004299			Rho GTPase activating protein 1						Rho protein signal transduction	cytosol|intracellular membrane-bounded organelle	SH3 domain binding|SH3/SH2 adaptor activity			skin(1)	1		Lung NSC(402;1.76e-12)|all_lung(304;1.3e-11)		GBM - Glioblastoma multiforme(35;5.17e-06)|BRCA - Breast invasive adenocarcinoma(625;0.00112)|Lung(87;0.153)														---	---	---	---
ARFGAP2	84364	broad.mit.edu	37	11	47189417	47189417	+	Intron	DEL	A	-	-	rs34204386		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47189417delA	uc001ndt.2	-						ARFGAP2_uc010rha.1_Intron|ARFGAP2_uc010rhb.1_Intron|ARFGAP2_uc001ndu.2_Intron|ARFGAP2_uc010rhc.1_Intron	NM_032389	NP_115765			ADP-ribosylation factor GTPase activating						protein transport|regulation of ARF GTPase activity|vesicle-mediated transport	Golgi membrane|nucleolus|plasma membrane	ARF GTPase activator activity|zinc ion binding			ovary(1)	1																		---	---	---	---
SLC39A13	91252	broad.mit.edu	37	11	47377894	47377895	+	Intron	DEL	CA	-	-	rs141558426		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47377894_47377895delCA	uc001nfd.2	+						SPI1_uc001nfb.1_Intron|SPI1_uc001nfc.1_Intron					RecName: Full=Zinc transporter ZIP13; AltName: Full=Zrt- and Irt-like protein 13;          Short=ZIP-13; AltName: Full=Solute carrier family 39 member 13; AltName: Full=LIV-1 subfamily of ZIP zinc transporter 9; AltName: Full=LZT-Hs9;						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity				0				Lung(87;0.0936)														---	---	---	---
SLC39A13	91252	broad.mit.edu	37	11	47415506	47415507	+	Intron	INS	-	A	A	rs72512059		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47415506_47415507insA	uc001nfd.2	+											RecName: Full=Zinc transporter ZIP13; AltName: Full=Zrt- and Irt-like protein 13;          Short=ZIP-13; AltName: Full=Solute carrier family 39 member 13; AltName: Full=LIV-1 subfamily of ZIP zinc transporter 9; AltName: Full=LZT-Hs9;						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity				0				Lung(87;0.0936)														---	---	---	---
CELF1	10658	broad.mit.edu	37	11	47510678	47510678	+	5'Flank	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47510678delA	uc001nfl.2	-						CELF1_uc001nfm.2_Intron|CELF1_uc001nfn.2_Intron|CELF1_uc001nfo.1_Intron|CELF1_uc010rhm.1_5'Flank|CELF1_uc001nfp.2_Intron|CELF1_uc001nfq.1_Intron|CELF1_uc001nfr.1_5'Flank	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																		---	---	---	---
NUP160	23279	broad.mit.edu	37	11	47839594	47839594	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47839594delT	uc001ngm.2	-						NUP160_uc009ylw.2_Intron	NM_015231	NP_056046			nucleoporin 160kDa						carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			ovary(4)|lung(1)|central_nervous_system(1)|skin(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	47913147	47913147	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47913147delA								NUP160 (43090 upstream) : PTPRJ (88963 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	48193640	48193641	+	IGR	DEL	AC	-	-	rs10769319	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48193640_48193641delAC								PTPRJ (1247 upstream) : OR4B1 (44721 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	48365048	48365048	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48365048delT								OR4C3 (17568 upstream) : OR4C45 (1854 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	48397286	48397286	+	IGR	DEL	T	-	-	rs78130555		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48397286delT								OR4C45 (23287 upstream) : OR4A47 (113059 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	49382576	49382576	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49382576delG								FOLH1 (152354 upstream) : LOC440040 (197504 downstream)																																			---	---	---	---
LOC440040	440040	broad.mit.edu	37	11	49782902	49782902	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49782902delT	uc010rhy.1	+						LOC440040_uc009ymb.2_Intron	NR_027044				SubName: Full=cDNA FLJ60249, highly similar to Metabotropic glutamate receptor 5;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	54941858	54941858	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:54941858delG								None (None upstream) : TRIM48 (87800 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	56610271	56610271	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56610271delT								OR9G4 (98984 upstream) : OR5AK2 (146118 downstream)																																			---	---	---	---
APLNR	187	broad.mit.edu	37	11	57002218	57002221	+	3'UTR	DEL	ACAC	-	-	rs140473375		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57002218_57002221delACAC	uc001njo.2	-	1					APLNR_uc001njn.3_Intron	NM_005161	NP_005152			apelin receptor							integral to plasma membrane	G-protein coupled receptor activity			lung(5)|ovary(1)	6																		---	---	---	---
SLC43A1	8501	broad.mit.edu	37	11	57283327	57283327	+	5'Flank	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57283327delC	uc001nkk.2	-						SLC43A1_uc001nkl.2_5'Flank	NM_003627	NP_003618			solute carrier family 43, member 1						cellular nitrogen compound metabolic process|ion transport	integral to plasma membrane	neutral amino acid transmembrane transporter activity				0																		---	---	---	---
CTNND1	1500	broad.mit.edu	37	11	57521525	57521527	+	Intron	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57521525_57521527delAAA	uc001nlh.1	+						CTNND1_uc001nlf.1_Intron|BTBD18_uc009ymm.2_5'Flank|BTBD18_uc010rjy.1_5'Flank	NM_001085466	NP_001078935			catenin, delta 1 isoform 3AC						adherens junction organization|cell junction assembly|negative regulation of canonical Wnt receptor signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	cytosol|midbody|nucleus	cadherin binding|protein binding|receptor binding			breast(4)|ovary(1)|kidney(1)	6		all_epithelial(135;0.155)																---	---	---	---
DTX4	23220	broad.mit.edu	37	11	58948505	58948505	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58948505delT	uc001nns.2	+						DTX4_uc001nnr.2_Intron	NM_015177	NP_055992			deltex 4 homolog						Notch signaling pathway	cytoplasm	zinc ion binding			lung(2)|central_nervous_system(1)	3		all_epithelial(135;0.125)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	59068431	59068431	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59068431delA								MPEG1 (87937 upstream) : OR5AN1 (63501 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	59255200	59255200	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59255200delA								OR4D10 (9362 upstream) : OR4D11 (15849 downstream)																																			---	---	---	---
STX3	6809	broad.mit.edu	37	11	59552803	59552803	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59552803delT	uc001nog.2	+						STX3_uc010rkx.1_Intron|STX3_uc010rky.1_Intron|STX3_uc009ymt.1_5'Flank	NM_004177	NP_004168			syntaxin 3						cellular response to oxidative stress|intracellular protein transport|neuron projection development|neurotransmitter transport	apical plasma membrane|azurophil granule|cell-cell junction|growth cone|integral to membrane|plasma membrane enriched fraction|SNARE complex|specific granule	arachidonic acid binding|SNAP receptor activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	59584749	59584750	+	IGR	DEL	TG	-	-	rs112748965		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59584749_59584750delTG								MRPL16 (6404 upstream) : GIF (11998 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	59656058	59656058	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59656058delG								TCN1 (22017 upstream) : PLAC1L (151690 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	59795412	59795412	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59795412delA								TCN1 (161371 upstream) : PLAC1L (12336 downstream)																																			---	---	---	---
MS4A1	931	broad.mit.edu	37	11	60227554	60227554	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60227554delA	uc001npp.2	+						MS4A1_uc009ymy.1_Intron|MS4A1_uc001npq.2_Intron|MS4A1_uc009yna.2_Intron|MS4A1_uc009ymz.2_Intron|MS4A1_uc010rlc.1_Intron	NM_152866	NP_690605			membrane-spanning 4-domains, subfamily A, member						B cell activation|immune response	integral to plasma membrane				ovary(3)|lung(2)	5					Ibritumomab(DB00078)|Rituximab(DB00073)|Tositumomab(DB00081)													---	---	---	---
C11orf64	283197	broad.mit.edu	37	11	60393713	60393714	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60393713_60393714delAA	uc001npt.2	+						C11orf64_uc001npu.2_Intron	NR_026946				Homo sapiens cDNA FLJ25394 fis, clone TST02552.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	60795584	60795584	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60795584delT								CD6 (7738 upstream) : CD5 (74346 downstream)																																			---	---	---	---
RAB3IL1	5866	broad.mit.edu	37	11	61683817	61683818	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61683817_61683818insA	uc001nso.2	-						RAB3IL1_uc001nsp.2_Intron	NM_013401	NP_037533			RAB3A interacting protein (rabin3)-like 1								protein binding			skin(2)|central_nervous_system(1)	3																		---	---	---	---
INCENP	3619	broad.mit.edu	37	11	61917391	61917392	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61917391_61917392insA	uc001nsw.1	+						INCENP_uc001nsx.1_Intron|INCENP_uc001nsy.1_Intron	NM_001040694	NP_001035784			inner centromere protein antigens 135/155kDa						chromosome segregation|cytokinesis|mitotic prometaphase	centromeric heterochromatin|condensed chromosome kinetochore|cytosol|microtubule|spindle	protein binding			lung(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	61926594	61926594	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61926594delA								INCENP (5959 upstream) : SCGB1D1 (31116 downstream)																																			---	---	---	---
INTS5	80789	broad.mit.edu	37	11	62414351	62414351	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62414351delA	uc001nud.2	-	2					GANAB_uc001nua.2_5'Flank|GANAB_uc001nub.2_5'Flank|GANAB_uc001nuc.2_5'Flank|GANAB_uc010rma.1_5'Flank|GANAB_uc010rmb.1_5'Flank	NM_030628	NP_085131			integrator complex subunit 5						snRNA processing	integral to membrane|integrator complex	protein binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	62727530	62727530	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62727530delT								CHRM1 (38518 upstream) : SLC22A6 (16540 downstream)																																			---	---	---	---
SLC22A10	387775	broad.mit.edu	37	11	62930798	62930799	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62930798_62930799delTT	uc010rmo.1	+											Homo sapiens mRNA for putative protein product of HMFN2567, complete cds.							integral to membrane	transmembrane transporter activity			ovary(2)	2																		---	---	---	---
PLA2G16	11145	broad.mit.edu	37	11	63345023	63345023	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63345023delA	uc001nxh.2	-						PLA2G16_uc001nxi.2_Intron|PLA2G16_uc009you.1_Intron	NM_007069	NP_009000			HRAS-like suppressor 3						lipid catabolic process	integral to membrane|perinuclear region of cytoplasm	hydrolase activity|protein binding			ovary(1)	1																		---	---	---	---
PLA2G16	11145	broad.mit.edu	37	11	63362079	63362079	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63362079delA	uc001nxh.2	-						PLA2G16_uc001nxi.2_Intron|PLA2G16_uc009you.1_Intron	NM_007069	NP_009000			HRAS-like suppressor 3						lipid catabolic process	integral to membrane|perinuclear region of cytoplasm	hydrolase activity|protein binding			ovary(1)	1																		---	---	---	---
ATL3	25923	broad.mit.edu	37	11	63429361	63429361	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63429361delA	uc001nxk.1	-						ATL3_uc010rms.1_Intron|ATL3_uc001nxl.1_Intron	NM_015459	NP_056274			atlastin 3						endoplasmic reticulum organization|Golgi organization|protein homooligomerization	endoplasmic reticulum membrane|integral to membrane	GTP binding|GTPase activity|identical protein binding			pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	63744773	63744773	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63744773delT								COX8A (759 upstream) : OTUB1 (8552 downstream)																																			---	---	---	---
MACROD1	28992	broad.mit.edu	37	11	63929815	63929815	+	Intron	DEL	A	-	-	rs71468653		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63929815delA	uc001nyh.2	-							NM_014067	NP_054786			MACRO domain containing 1												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	64205499	64205499	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64205499delT								RPS6KA4 (65813 upstream) : SLC22A11 (117599 downstream)																																			---	---	---	---
C11orf85	283129	broad.mit.edu	37	11	64724111	64724111	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64724111delA	uc001ocb.1	-						C11orf85_uc001occ.1_Intron|C11orf85_uc001ocd.1_Intron	NM_001037225	NP_001032302			hypothetical protein LOC283129												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	64752335	64752336	+	IGR	DEL	TT	-	-	rs111294051		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64752335_64752336delTT								C11orf85 (12778 upstream) : BATF2 (3081 downstream)																																			---	---	---	---
SNX15	29907	broad.mit.edu	37	11	64797974	64797976	+	Intron	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64797974_64797976delTTT	uc001oci.3	+						SNX15_uc009ypy.2_Intron|SNX15_uc001ocj.2_Intron|SNX15_uc001ock.2_Intron	NM_013306	NP_037438			sorting nexin 15 isoform A						cell communication|intracellular protein transport	cytoplasmic vesicle membrane|cytosol	phosphatidylinositol binding|protein transporter activity			ovary(1)	1																		---	---	---	---
PCNXL3	399909	broad.mit.edu	37	11	65392081	65392081	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65392081delG	uc001oey.2	+						PCNXL3_uc009yqn.2_5'Flank|PCNXL3_uc001oez.2_5'Flank	NM_032223	NP_115599			pecanex-like 3							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	65750565	65750566	+	IGR	INS	-	T	T	rs150526317	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65750565_65750566insT								SART1 (2959 upstream) : EIF1AD (13451 downstream)																																			---	---	---	---
BANF1	8815	broad.mit.edu	37	11	65770687	65770687	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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																		---	---	---	---
PACS1	55690	broad.mit.edu	37	11	65926909	65926910	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65926909_65926910delAA	uc001oha.1	+						PACS1_uc001ogz.1_Intron	NM_018026	NP_060496			phosphofurin acidic cluster sorting protein 1						interspecies interaction between organisms|regulation of defense response to virus by virus|viral reproduction	cytosol	protein binding			ovary(6)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	66218923	66218923	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66218923delA								MRPL11 (12613 upstream) : PELI3 (15413 downstream)																																			---	---	---	---
RBM4	5936	broad.mit.edu	37	11	66398763	66398763	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66398763delT	uc009yrj.2	+						RBM4_uc009yrk.2_Intron	NM_002896	NP_002887			RNA binding motif protein 4						circadian regulation of gene expression|entrainment of circadian clock by photoperiod|mRNA processing|negative regulation of translation in response to stress|negative regulation of translation involved in gene silencing by miRNA|negative regulation of translational initiation|positive regulation of muscle cell differentiation|regulation of alternative nuclear mRNA splicing, via spliceosome|regulation of nucleocytoplasmic transport|RNA splicing|stress-activated MAPK cascade	nuclear speck|nucleolus|stress granule	miRNA binding|mRNA 3'-UTR binding|nucleotide binding|protein binding|zinc ion binding			ovary(1)	1				Lung(977;0.0112)|LUSC - Lung squamous cell carcinoma(976;0.0266)														---	---	---	---
C11orf80	79703	broad.mit.edu	37	11	66551477	66551478	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66551477_66551478insT	uc001ojf.2	+						C11orf80_uc001ojg.2_Intron|C11orf80_uc001ojh.2_Intron|C11orf80_uc001oji.2_Intron|C11orf80_uc010rpk.1_Intron	NM_024650	NP_078926			hypothetical protein LOC79703												0																		---	---	---	---
ADRBK1	156	broad.mit.edu	37	11	67035829	67035829	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67035829delT	uc009yrn.1	+						ADRBK1_uc009yrm.1_Intron	NM_001619	NP_001610			beta-adrenergic receptor kinase 1						activation of phospholipase C activity|cardiac muscle contraction|desensitization of G-protein coupled receptor protein signaling pathway|muscarinic acetylcholine receptor signaling pathway|negative regulation of striated muscle contraction|negative regulation of the force of heart contraction by chemical signal|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|positive regulation of catecholamine secretion|tachykinin receptor signaling pathway	cytosol|soluble fraction	alpha-2A adrenergic receptor binding|ATP binding|beta-adrenergic receptor kinase activity|Edg-2 lysophosphatidic acid receptor binding|G-protein coupled receptor kinase activity|signal transducer activity			large_intestine(1)	1			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)		Adenosine triphosphate(DB00171)													---	---	---	---
CARNS1	57571	broad.mit.edu	37	11	67192333	67192336	+	3'UTR	DEL	CACA	-	-	rs68075271		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67192333_67192336delCACA	uc009yrp.2	+	9					CARNS1_uc001olc.3_3'UTR	NM_020811	NP_065862			ATP-grasp domain containing 1						carnosine biosynthetic process		ATP binding|carnosine synthase activity|metal ion binding				0																		---	---	---	---
AIP	9049	broad.mit.edu	37	11	67254767	67254769	+	Intron	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67254767_67254769delTTT	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	68001777	68001777	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68001777delT								SUV420H1 (20709 upstream) : C11orf24 (27028 downstream)																																			---	---	---	---
LRP5	4041	broad.mit.edu	37	11	68187009	68187011	+	Intron	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68187009_68187011delTTT	uc001ont.2	+						LRP5_uc009ysg.2_Intron	NM_002335	NP_002326			low density lipoprotein receptor-related protein						adipose tissue development|bone marrow development|bone morphogenesis|canonical Wnt receptor signaling pathway|cholesterol homeostasis|endocytosis|glucose catabolic process|negative regulation of osteoblast differentiation|negative regulation of protein serine/threonine kinase activity|positive regulation of fat cell differentiation|positive regulation of mesenchymal cell proliferation|positive regulation of mitosis|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of canonical Wnt receptor signaling pathway|retina morphogenesis in camera-type eye|retinal blood vessel morphogenesis|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	endoplasmic reticulum|integral to membrane|plasma membrane|receptor complex	protein binding|receptor activity			lung(2)|skin(2)|ovary(1)|pancreas(1)|breast(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	68644191	68644192	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68644191_68644192delAA								CPT1A (34792 upstream) : MRPL21 (14555 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	69162602	69162603	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69162602_69162603insT								MYEOV (6153 upstream) : CCND1 (293270 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	69383301	69383302	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69383301_69383302delTG								MYEOV (226852 upstream) : CCND1 (72571 downstream)																																			---	---	---	---
PPFIA1	8500	broad.mit.edu	37	11	70120776	70120776	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70120776delT	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	70243134	70243134	+	5'Flank	DEL	T	-	-	rs149887374		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70243134delT	uc001opu.2	+						CTTN_uc001opv.3_5'Flank|CTTN_uc001opw.3_5'Flank|uc001opt.1_Intron	NM_138565	NP_612632			cortactin isoform b							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	70335153	70335153	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70335153delA	uc001oqc.2	-						SHANK2_uc010rqn.1_Intron|SHANK2_uc001opz.2_Intron|uc009ysn.1_Intron|SHANK2_uc001opy.2_Intron	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)															---	---	---	---
SHANK2	22941	broad.mit.edu	37	11	70490023	70490023	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70490023delG	uc001oqc.2	-						SHANK2_uc010rqn.1_Intron|SHANK2_uc001opz.2_Intron|uc009ysn.1_Intron|SHANK2_uc010rqp.1_Intron	NM_012309	NP_036441			SH3 and multiple ankyrin repeat domains 2						intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)															---	---	---	---
NUMA1	4926	broad.mit.edu	37	11	71787831	71787832	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71787831_71787832delAA	uc001orl.1	-						NUMA1_uc001ork.1_Intron|NUMA1_uc001orm.1_Intron|NUMA1_uc001oro.1_Intron|NUMA1_uc001orq.2_Intron	NM_006185	NP_006176			nuclear mitotic apparatus protein 1						G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization	chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole	protein binding|structural molecule activity			ovary(3)|lung(2)|skin(2)|central_nervous_system(1)	8								T	RARA	APL								---	---	---	---
PDE2A	5138	broad.mit.edu	37	11	72334673	72334673	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72334673delC	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)													---	---	---	---
FCHSD2	9873	broad.mit.edu	37	11	72699853	72699853	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72699853delA	uc009ytl.2	-						FCHSD2_uc010rrg.1_Intron|FCHSD2_uc001oth.3_Intron|FCHSD2_uc001oti.2_Intron	NM_014824	NP_055639			FCH and double SH3 domains 2								protein binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(5;3.3e-05)															---	---	---	---
FCHSD2	9873	broad.mit.edu	37	11	72765827	72765827	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72765827delC	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	73229940	73229940	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73229940delA	uc001otz.1	-						FAM168A_uc001oty.1_Intron|FAM168A_uc009ytp.1_Intron	NM_015159	NP_055974			hypothetical protein LOC23201												0																		---	---	---	---
XRRA1	143570	broad.mit.edu	37	11	74565900	74565901	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74565900_74565901insA	uc009yub.2	-						XRRA1_uc001ovm.2_Intron|XRRA1_uc001ovn.2_Intron|XRRA1_uc001ovo.2_Intron|XRRA1_uc001ovq.3_Intron|XRRA1_uc001ovp.3_Intron|XRRA1_uc001ovr.2_Intron|XRRA1_uc001ovs.1_Intron	NM_182969	NP_892014			X-ray radiation resistance associated 1						response to X-ray	cytoplasm|nucleus				central_nervous_system(1)	1																		---	---	---	---
XRRA1	143570	broad.mit.edu	37	11	74656099	74656099	+	5'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74656099delT	uc009yub.2	-	2					XRRA1_uc001ovm.2_RNA|XRRA1_uc001ovo.2_5'UTR|XRRA1_uc001ovq.3_5'UTR|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																		---	---	---	---
OR2AT4	341152	broad.mit.edu	37	11	74801979	74801979	+	5'Flank	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74801979delG	uc010rro.1	-							NM_001005285	NP_001005285			olfactory receptor, family 2, subfamily AT,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1																		---	---	---	---
ARRB1	408	broad.mit.edu	37	11	74978643	74978643	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74978643delC	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	75466333	75466333	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75466333delA								MOGAT2 (24003 upstream) : DGAT2 (13445 downstream)																																			---	---	---	---
UVRAG	7405	broad.mit.edu	37	11	75839002	75839002	+	Intron	DEL	A	-	-	rs75226887		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75839002delA	uc001oxc.2	+						UVRAG_uc010rrw.1_Intron|UVRAG_uc001oxd.2_Intron|UVRAG_uc010rrx.1_Intron|UVRAG_uc010rry.1_Intron	NM_003369	NP_003360			UV radiation resistance associated						DNA repair|positive regulation of autophagy	early endosome|late endosome|lysosome	protein binding			skin(4)|lung(2)	6																		---	---	---	---
PRKRIR	5612	broad.mit.edu	37	11	76083932	76083932	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76083932delA	uc001oxh.1	-							NM_004705	NP_004696			protein-kinase, interferon-inducible double						negative regulation of cell proliferation|response to stress|signal transduction		DNA binding|metal ion binding|protein dimerization activity			ovary(2)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	76323683	76323683	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76323683delT								C11orf30 (61095 upstream) : LRRC32 (44886 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	76456095	76456095	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76456095delT								GUCY2E (23262 upstream) : TSKU (38190 downstream)																																			---	---	---	---
RSF1	51773	broad.mit.edu	37	11	77436580	77436580	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77436580delA	uc001oyn.2	-							NM_016578	NP_057662			remodeling and spacing factor 1						CenH3-containing nucleosome assembly at centromere|negative regulation of DNA binding|negative regulation of transcription, DNA-dependent|nucleosome positioning|positive regulation of transcription, DNA-dependent|positive regulation of viral transcription|transcription initiation, DNA-dependent	RSF complex	histone binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(2)	4	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)															---	---	---	---
ALG8	79053	broad.mit.edu	37	11	77851749	77851749	+	5'Flank	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77851749delA	uc001oza.1	-						ALG8_uc001oyz.1_5'Flank|ALG8_uc009yux.1_5'Flank|ALG8_uc009yuy.1_5'Flank	NM_024079	NP_076984			dolichyl pyrophosphate Glc1Man9GlcNAc2						dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	alpha-1,3-mannosyltransferase activity|dolichyl-phosphate-glucose-glycolipid alpha-glucosyltransferase activity			ovary(2)|pancreas(1)	3	all_cancers(14;3.62e-19)|all_epithelial(13;1.27e-21)|Breast(9;8.51e-17)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;9.66e-25)															---	---	---	---
Unknown	0	broad.mit.edu	37	11	78299283	78299283	+	IGR	DEL	A	-	-	rs74788485		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78299283delA								NARS2 (13374 upstream) : ODZ4 (65046 downstream)																																			---	---	---	---
ODZ4	26011	broad.mit.edu	37	11	78559198	78559200	+	Intron	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78559198_78559200delTTT	uc001ozl.3	-							NM_001098816	NP_001092286			odz, odd Oz/ten-m homolog 4						signal transduction	integral to membrane				ovary(2)|pancreas(2)	4																		---	---	---	---
ODZ4	26011	broad.mit.edu	37	11	78783530	78783531	+	Intron	DEL	AA	-	-	rs10550784		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78783530_78783531delAA	uc001ozl.3	-						ODZ4_uc009yvc.2_Intron	NM_001098816	NP_001092286			odz, odd Oz/ten-m homolog 4						signal transduction	integral to membrane				ovary(2)|pancreas(2)	4																		---	---	---	---
ODZ4	26011	broad.mit.edu	37	11	78999939	78999939	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78999939delA	uc001ozl.3	-							NM_001098816	NP_001092286			odz, odd Oz/ten-m homolog 4						signal transduction	integral to membrane				ovary(2)|pancreas(2)	4																		---	---	---	---
ODZ4	26011	broad.mit.edu	37	11	79091355	79091355	+	Intron	DEL	A	-	-	rs113989429		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79091355delA	uc001ozl.3	-							NM_001098816	NP_001092286			odz, odd Oz/ten-m homolog 4						signal transduction	integral to membrane				ovary(2)|pancreas(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	80266283	80266284	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:80266283_80266284delTC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	80441506	80441507	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:80441506_80441507delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	81732534	81732534	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:81732534delA	uc001ozo.1	-											Homo sapiens cDNA clone IMAGE:5298883.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	87044469	87044469	+	IGR	DEL	A	-	-	rs73531653	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87044469delA								TMEM135 (9901 upstream) : RAB38 (801962 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	87821836	87821836	+	IGR	DEL	T	-	-	rs146096493	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87821836delT								TMEM135 (787268 upstream) : RAB38 (24595 downstream)																																			---	---	---	---
GRM5	2915	broad.mit.edu	37	11	88372349	88372349	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88372349delA	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	89832190	89832191	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89832190_89832191delAC								UBTFL1 (11892 upstream) : NAALAD2 (35627 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	90324160	90324161	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:90324160_90324161insT								CHORDC1 (367628 upstream) : MIR1261 (278128 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	90375351	90375351	+	IGR	DEL	T	-	-	rs11376432		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:90375351delT								CHORDC1 (418819 upstream) : MIR1261 (226938 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	90954889	90954890	+	IGR	INS	-	CTCTA	CTCTA	rs147579472	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:90954889_90954890insCTCTA								MIR1261 (352519 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	91116223	91116224	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:91116223_91116224insA								MIR1261 (513853 upstream) : FAT3 (969038 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	92081303	92081303	+	IGR	DEL	T	-	-	rs77297950		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92081303delT								None (None upstream) : FAT3 (3959 downstream)																																			---	---	---	---
SLC36A4	120103	broad.mit.edu	37	11	92896062	92896062	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92896062delT	uc001pdn.2	-						SLC36A4_uc001pdm.2_Intron	NM_152313	NP_689526			solute carrier family 36 (proton/amino acid						L-alanine transport|proline transport|tryptophan transport	integral to membrane	symporter activity			ovary(2)|upper_aerodigestive_tract(1)	3		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	93287186	93287186	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93287186delA								C11orf75 (10640 upstream) : KIAA1731 (107630 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	93336548	93336555	+	IGR	DEL	TTCCTTTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93336548_93336555delTTCCTTTT								C11orf75 (60002 upstream) : KIAA1731 (58261 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	93612766	93612766	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93612766delC								C11orf90 (29098 upstream) : HEPHL1 (141612 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	94064514	94064514	+	IGR	DEL	T	-	-	rs35780075		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94064514delT								FOLR4 (23657 upstream) : GPR83 (45963 downstream)																																			---	---	---	---
SESN3	143686	broad.mit.edu	37	11	94930610	94930612	+	Intron	DEL	TTT	-	-	rs138559501		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94930610_94930612delTTT	uc001pfk.1	-						SESN3_uc010rug.1_Intron|SESN3_uc001pfl.2_Intron	NM_144665	NP_653266			sestrin 3						cell cycle arrest	nucleus					0		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)		BRCA - Breast invasive adenocarcinoma(274;0.234)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	95169184	95169185	+	IGR	INS	-	A	A	rs145071288	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95169184_95169185insA								SESN3 (203479 upstream) : FAM76B (332921 downstream)																																			---	---	---	---
CEP57	9702	broad.mit.edu	37	11	95559765	95559765	+	Intron	DEL	A	-	-	rs111590430		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95559765delA	uc001pfp.1	+						CEP57_uc010ruh.1_Intron|CEP57_uc010rui.1_Intron|CEP57_uc009ywn.1_Intron|CEP57_uc001pfq.1_Intron|CEP57_uc001pfr.1_Intron	NM_014679	NP_055494			translokin						fibroblast growth factor receptor signaling pathway|G2/M transition of mitotic cell cycle|protein import into nucleus, translocation|spermatid development	centrosome|cytosol|Golgi apparatus|microtubule|nucleus	fibroblast growth factor binding|protein homodimerization activity			ovary(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)												Mosaic_Variegated_Aneuploidy_Syndrome				---	---	---	---
CEP57	9702	broad.mit.edu	37	11	95561203	95561203	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95561203delT	uc001pfp.1	+						CEP57_uc010ruh.1_Intron|CEP57_uc010rui.1_Intron|CEP57_uc009ywn.1_Intron|CEP57_uc001pfq.1_Intron|CEP57_uc001pfr.1_Intron	NM_014679	NP_055494			translokin						fibroblast growth factor receptor signaling pathway|G2/M transition of mitotic cell cycle|protein import into nucleus, translocation|spermatid development	centrosome|cytosol|Golgi apparatus|microtubule|nucleus	fibroblast growth factor binding|protein homodimerization activity			ovary(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)												Mosaic_Variegated_Aneuploidy_Syndrome				---	---	---	---
MAML2	84441	broad.mit.edu	37	11	95910197	95910197	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95910197delT	uc001pfw.1	-							NM_032427	NP_115803			mastermind-like 2						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity		CRTC1/MAML2(516)|CRTC3/MAML2(26)	salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1)	546		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)						T	MECT1|CRTC3	salivary gland mucoepidermoid								---	---	---	---
Unknown	0	broad.mit.edu	37	11	96724360	96724360	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:96724360delT								JRKL (597633 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	97770949	97770950	+	IGR	INS	-	G	G	rs140438624	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:97770949_97770950insG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	97876066	97876066	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:97876066delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	98115595	98115595	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:98115595delT								None (None upstream) : CNTN5 (776276 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	98379154	98379154	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:98379154delA								None (None upstream) : CNTN5 (512717 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	98739085	98739086	+	IGR	INS	-	AC	AC	rs149415441	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:98739085_98739086insAC								None (None upstream) : CNTN5 (152785 downstream)																																			---	---	---	---
CNTN5	53942	broad.mit.edu	37	11	99663270	99663271	+	Intron	DEL	GT	-	-	rs111267307		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99663270_99663271delGT	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	99770833	99770833	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99770833delT	uc001pga.2	+						CNTN5_uc009ywv.1_Intron|CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron	NM_014361	NP_055176			contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	101268749	101268750	+	IGR	INS	-	AGATAGAT	AGATAGAT	rs141822336	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101268749_101268750insAGATAGAT								PGR (268205 upstream) : TRPC6 (53546 downstream)																																			---	---	---	---
MMP13	4322	broad.mit.edu	37	11	102816205	102816205	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102816205delT	uc001phl.2	-							NM_002427	NP_002418			matrix metalloproteinase 13 preproprotein						collagen catabolic process|proteolysis	extracellular space	metalloendopeptidase activity|zinc ion binding			ovary(2)|skin(1)	3		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0144)														---	---	---	---
DYNC2H1	79659	broad.mit.edu	37	11	102985880	102985880	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102985880delT	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	103114406	103114407	+	Intron	INS	-	TT	TT			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103114406_103114407insTT	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	103831582	103831583	+	Intron	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103831582_103831583delAG	uc001phq.2	-						PDGFD_uc001php.2_Intron	NM_025208	NP_079484			platelet derived growth factor D isoform 1						positive regulation of cell division	endoplasmic reticulum lumen|extracellular region|Golgi membrane	growth factor activity			upper_aerodigestive_tract(1)|large_intestine(1)	2		Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Melanoma(852;0.0563)|all_neural(303;0.165)		BRCA - Breast invasive adenocarcinoma(274;0.00136)|Epithelial(105;0.111)														---	---	---	---
PDGFD	80310	broad.mit.edu	37	11	103871040	103871040	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103871040delA	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	104342467	104342467	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104342467delG								PDGFD (307440 upstream) : CASP12 (413975 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	104388633	104388633	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104388633delT								PDGFD (353606 upstream) : CASP12 (367809 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	104505146	104505147	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104505146_104505147delAC								PDGFD (470119 upstream) : CASP12 (251295 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	104524460	104524461	+	IGR	DEL	AC	-	-	rs146111430		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104524460_104524461delAC								PDGFD (489433 upstream) : CASP12 (231981 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	104858592	104858592	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104858592delC								CASP4 (19267 upstream) : CASP5 (6375 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	105344108	105344108	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105344108delA								CARD18 (334302 upstream) : GRIA4 (136692 downstream)																																			---	---	---	---
KBTBD3	143879	broad.mit.edu	37	11	105929470	105929470	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105929470delT	uc001pja.2	-						KBTBD3_uc001pjb.2_Intron|KBTBD3_uc009yxm.2_Intron	NM_198439	NP_940841			BTB and kelch domain containing 3											ovary(1)|central_nervous_system(1)	2		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.43e-05)|Epithelial(105;0.00418)|all cancers(92;0.0299)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	106001030	106001031	+	IGR	INS	-	T	T	rs11407212		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106001030_106001031insT								AASDHPPT (31611 upstream) : GUCY1A2 (556879 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	107363049	107363052	+	IGR	DEL	TTTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107363049_107363052delTTTT								CWF19L2 (34477 upstream) : ALKBH8 (10402 downstream)																																			---	---	---	---
CUL5	8065	broad.mit.edu	37	11	107953014	107953015	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107953014_107953015delTT	uc001pjv.2	+						CUL5_uc001pju.2_Intron	NM_003478	NP_003469			Vasopressin-activated calcium-mobilizing						cell cycle arrest|cell proliferation|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|ubiquitin-dependent protein catabolic process|viral reproduction	cullin-RING ubiquitin ligase complex|cytosol	calcium channel activity|receptor activity|ubiquitin protein ligase binding			ovary(1)	1		all_cancers(61;7.09e-10)|all_epithelial(67;2.97e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|Melanoma(852;4.48e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;3.58e-05)|Epithelial(105;4.68e-05)|all cancers(92;0.00122)|OV - Ovarian serous cystadenocarcinoma(223;0.217)														---	---	---	---
ACAT1	38	broad.mit.edu	37	11	108014946	108014946	+	Intron	DEL	A	-	-	rs71893124		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108014946delA	uc001pjy.2	+							NM_000019	NP_000010			acetyl-Coenzyme A acetyltransferase 1 precursor						acetoacetic acid biosynthetic process|branched chain family amino acid catabolic process|ketone body biosynthetic process|ketone body catabolic process	mitochondrial matrix	acetyl-CoA C-acetyltransferase activity|metal ion binding			ovary(3)	3		all_cancers(61;6.41e-10)|all_epithelial(67;2.83e-06)|Melanoma(852;1.46e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;2.96e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.00108)|OV - Ovarian serous cystadenocarcinoma(223;0.192)	Sulfasalazine(DB00795)													---	---	---	---
NPAT	4863	broad.mit.edu	37	11	108063682	108063682	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108063682delA	uc001pjz.3	-							NM_002519	NP_002510			nuclear protein,  ataxia-telangiectasia locus						positive regulation of transcription, DNA-dependent|regulation of transcription involved in G1/S phase of mitotic cell cycle	Cajal body	protein C-terminus binding|protein N-terminus binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity			ovary(2)	2		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)														---	---	---	---
DDX10	1662	broad.mit.edu	37	11	108586829	108586830	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108586829_108586830insT	uc001pkm.2	+						DDX10_uc001pkl.1_Intron	NM_004398	NP_004389			DEAD (Asp-Glu-Ala-Asp) box polypeptide 10								ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity			breast(2)|lung(1)|prostate(1)	4		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)				T	NUP98	AML*								---	---	---	---
DDX10	1662	broad.mit.edu	37	11	108781528	108781529	+	Intron	INS	-	TGTG	TGTG	rs139983666	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108781528_108781529insTGTG	uc001pkm.2	+						DDX10_uc001pkl.1_Intron	NM_004398	NP_004389			DEAD (Asp-Glu-Ala-Asp) box polypeptide 10								ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity			breast(2)|lung(1)|prostate(1)	4		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)				T	NUP98	AML*								---	---	---	---
DDX10	1662	broad.mit.edu	37	11	108788854	108788854	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108788854delT	uc001pkm.2	+						DDX10_uc001pkl.1_3'UTR	NM_004398	NP_004389			DEAD (Asp-Glu-Ala-Asp) box polypeptide 10								ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity			breast(2)|lung(1)|prostate(1)	4		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)				T	NUP98	AML*								---	---	---	---
FDX1	2230	broad.mit.edu	37	11	110306545	110306545	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110306545delT	uc001pkx.2	+							NM_004109	NP_004100			ferredoxin 1 precursor						electron transport chain|transport	mitochondrial matrix	2 iron, 2 sulfur cluster binding|electron carrier activity|iron ion binding				0		all_cancers(61;1.59e-12)|all_epithelial(67;8.38e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.01e-06)|BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|all cancers(92;5.27e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0384)|Colorectal(284;0.228)	Mitotane(DB00648)													---	---	---	---
ARHGAP20	57569	broad.mit.edu	37	11	110549560	110549560	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110549560delT	uc001pkz.1	-						ARHGAP20_uc001pky.1_Intron|ARHGAP20_uc009yyb.1_Intron|ARHGAP20_uc001pla.1_Intron	NM_020809	NP_065860			Rho GTPase activating protein 20						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(3)|kidney(2)	5		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	111285956	111285956	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111285956delG	uc001plh.1	-											Homo sapiens, clone IMAGE:4694422, mRNA.																														---	---	---	---
PPP2R1B	5519	broad.mit.edu	37	11	111609606	111609607	+	3'UTR	INS	-	TG	TG	rs7131029		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111609606_111609607insTG	uc001plx.1	-	15					PPP2R1B_uc001plw.1_Intron|PPP2R1B_uc010rwi.1_Intron|PPP2R1B_uc009yyf.1_5'Flank|PPP2R1B_uc010rwj.1_3'UTR|PPP2R1B_uc010rwk.1_3'UTR|PPP2R1B_uc010rwl.1_3'UTR	NM_002716	NP_002707			beta isoform of regulatory subunit A, protein								protein binding				0		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|Epithelial(105;2.36e-06)|all cancers(92;3.78e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0761)														---	---	---	---
DIXDC1	85458	broad.mit.edu	37	11	111799130	111799130	+	5'Flank	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111799130delG	uc001pmj.2	+											SubName: Full=DIXDC1 protein; SubName: Full=HCG2038196; Flags: Fragment;						multicellular organismal development|positive regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytosol|focal adhesion	actin binding|gamma-tubulin binding|signal transducer activity			ovary(1)	1		all_cancers(61;7.58e-15)|all_epithelial(67;5.42e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;2.99e-07)|BRCA - Breast invasive adenocarcinoma(274;6.72e-07)|all cancers(92;6.25e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0548)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	111975949	111975949	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111975949delT								SDHD (9432 upstream) : IL18 (38027 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	112160060	112160060	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112160060delT	uc001pnm.1	+											full-length cDNA clone CS0DF020YJ04 of Fetal brain of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	112535502	112535502	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112535502delA								PTS (394825 upstream) : NCAM1 (296493 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	112540065	112540065	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112540065delT								PTS (399388 upstream) : NCAM1 (291930 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	112606977	112606978	+	IGR	INS	-	TC	TC	rs72203711		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112606977_112606978insTC								PTS (466300 upstream) : NCAM1 (225017 downstream)																																			---	---	---	---
NCAM1	4684	broad.mit.edu	37	11	112979434	112979435	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112979434_112979435insT	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)														---	---	---	---
TTC12	54970	broad.mit.edu	37	11	113195202	113195203	+	Intron	DEL	GC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113195202_113195203delGC	uc001pnu.2	+						TTC12_uc001pnv.2_Intron|TTC12_uc001pnw.2_Intron|TTC12_uc001pnx.2_Intron	NM_017868	NP_060338			tetratricopeptide repeat domain 12								binding			pancreas(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4		all_cancers(61;2.73e-16)|all_epithelial(67;8.64e-10)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.183)|Renal(330;0.187)		BRCA - Breast invasive adenocarcinoma(274;5.3e-06)|Epithelial(105;8.37e-05)|all cancers(92;0.000694)														---	---	---	---
NNMT	4837	broad.mit.edu	37	11	114162844	114162844	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114162844delT	uc001por.1	+							NM_006169	NP_006160			nicotinamide N-methyltransferase						xenobiotic metabolic process	cytosol	nicotinamide N-methyltransferase activity|pyridine N-methyltransferase activity			ovary(1)	1		all_cancers(61;4.83e-16)|all_epithelial(67;7.28e-09)|all_hematologic(158;0.000135)|Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0906)		BRCA - Breast invasive adenocarcinoma(274;2.79e-06)|Epithelial(105;1.32e-05)|all cancers(92;0.000144)|OV - Ovarian serous cystadenocarcinoma(223;0.128)	Niacin(DB00627)													---	---	---	---
CADM1	23705	broad.mit.edu	37	11	115069231	115069231	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115069231delA	uc001ppi.3	-						CADM1_uc001ppf.3_Intron|CADM1_uc001ppk.3_Intron|CADM1_uc001ppj.3_Intron|CADM1_uc001pph.3_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)														---	---	---	---
CADM1	23705	broad.mit.edu	37	11	115210636	115210636	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115210636delA	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	115565175	115565176	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115565175_115565176delTC								CADM1 (189934 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	115580382	115580382	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115580382delT								CADM1 (205141 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	115924237	115924237	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115924237delA								CADM1 (548996 upstream) : BUD13 (694651 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	116504738	116504739	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116504738_116504739insA								None (None upstream) : BUD13 (114149 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	117001759	117001759	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117001759delA								SIK3 (32766 upstream) : PAFAH1B2 (13281 downstream)																																			---	---	---	---
CEP164	22897	broad.mit.edu	37	11	117241635	117241636	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117241635_117241636delAA	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	117375416	117375416	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117375416delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	117878119	117878120	+	IGR	DEL	TT	-	-	rs78257724		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117878119_117878120delTT								IL10RA (5923 upstream) : TMPRSS4 (69607 downstream)																																			---	---	---	---
SCN2B	6327	broad.mit.edu	37	11	118047235	118047235	+	5'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118047235delA	uc001psf.2	-	1						NM_004588	NP_004579			sodium channel, voltage-gated, type II, beta						synaptic transmission	voltage-gated sodium channel complex	voltage-gated sodium channel activity				0	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.19e-05)|Epithelial(105;0.00117)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	118053497	118053497	+	IGR	DEL	T	-	-	rs112086298		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118053497delT								SCN2B (6160 upstream) : AMICA1 (10945 downstream)																																			---	---	---	---
TREH	11181	broad.mit.edu	37	11	118530100	118530100	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118530100delG	uc001pty.1	-	12	1456	c.1411delC	c.(1411-1413)CTGfs	p.L471fs	TREH_uc009zaj.1_Frame_Shift_Del_p.L440fs|TREH_uc001ptz.1_Frame_Shift_Del_p.L348fs	NM_007180	NP_009111	O43280	TREA_HUMAN	trehalase precursor	471					polysaccharide digestion|trehalose catabolic process	anchored to plasma membrane	alpha,alpha-trehalase activity			pancreas(1)	1	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.16e-05)												OREG0021385	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	118912763	118912763	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118912763delT								SLC37A4 (11147 upstream) : HYOU1 (2133 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	119286943	119286943	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119286943delG	uc001pwo.2	+						uc001pwp.1_Intron					Homo sapiens cDNA FLJ40501 fis, clone TESTI2045171.																														---	---	---	---
GRIK4	2900	broad.mit.edu	37	11	120390586	120390589	+	Intron	DEL	TTTG	-	-	rs2510874		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120390586_120390589delTTTG	uc001pxn.2	+							NM_014619	NP_055434			glutamate receptor KA1 precursor						glutamate signaling pathway|synaptic transmission	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|central_nervous_system(1)	3		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)	L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	120860737	120860738	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120860737_120860738delAA								GRIK4 (3768 upstream) : TBCEL (34065 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	121238644	121238644	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121238644delA								SC5DL (54527 upstream) : SORL1 (84317 downstream)																																			---	---	---	---
SORL1	6653	broad.mit.edu	37	11	121403397	121403398	+	Intron	DEL	TT	-	-	rs35892410		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121403397_121403398delTT	uc001pxx.2	+							NM_003105	NP_003096			sortilin-related receptor containing LDLR class						cholesterol metabolic process|lipid transport|receptor-mediated endocytosis	integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|transmembrane receptor activity			ovary(5)|breast(4)|large_intestine(2)|skin(2)|central_nervous_system(1)|pancreas(1)	15		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)														---	---	---	---
SORL1	6653	broad.mit.edu	37	11	121452256	121452256	+	Intron	DEL	A	-	-	rs74619929		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121452256delA	uc001pxx.2	+						SORL1_uc010rzp.1_Intron	NM_003105	NP_003096			sortilin-related receptor containing LDLR class						cholesterol metabolic process|lipid transport|receptor-mediated endocytosis	integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|transmembrane receptor activity			ovary(5)|breast(4)|large_intestine(2)|skin(2)|central_nervous_system(1)|pancreas(1)	15		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)														---	---	---	---
LOC399959	399959	broad.mit.edu	37	11	122031408	122031409	+	Intron	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122031408_122031409delTG	uc009zba.2	-							NR_024430				Homo sapiens cDNA FLJ34394 fis, clone HCHON2000676.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	122292032	122292032	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122292032delA								LOC399959 (53565 upstream) : UBASH3B (234366 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	124315228	124315228	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124315228delA								OR8B8 (4247 upstream) : OR8B12 (97392 downstream)																																			---	---	---	---
PKNOX2	63876	broad.mit.edu	37	11	125248871	125248872	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125248871_125248872delTT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	125310281	125310281	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125310281delA								PKNOX2 (6998 upstream) : FEZ1 (5369 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	125677069	125677070	+	IGR	DEL	CA	-	-	rs145325623		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125677069_125677070delCA								PATE3 (15576 upstream) : PATE4 (26141 downstream)																																			---	---	---	---
KIRREL3	84623	broad.mit.edu	37	11	126479992	126479992	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126479992delT	uc001qea.2	-						KIRREL3_uc001qeb.2_Intron|KIRREL3_uc001qec.1_Intron|KIRREL3_uc001qed.3_Intron	NM_032531	NP_115920			kin of IRRE like 3 isoform 1						hemopoiesis	extracellular region|integral to membrane|plasma membrane	protein binding			ovary(3)	3	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)														---	---	---	---
KIRREL3	84623	broad.mit.edu	37	11	126797125	126797128	+	Intron	DEL	CACA	-	-	rs35347795		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126797125_126797128delCACA	uc001qea.2	-						KIRREL3_uc001qeb.2_Intron|KIRREL3_uc001qec.1_Intron|KIRREL3_uc001qed.3_Intron	NM_032531	NP_115920			kin of IRRE like 3 isoform 1						hemopoiesis	extracellular region|integral to membrane|plasma membrane	protein binding			ovary(3)	3	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	127398885	127398885	+	IGR	DEL	T	-	-	rs5795574		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127398885delT								KIRREL3 (525530 upstream) : ETS1 (929771 downstream)																																			---	---	---	---
FLI1	2313	broad.mit.edu	37	11	128563409	128563409	+	5'Flank	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128563409delC	uc010sbu.1	+						FLI1_uc010sbt.1_Intron|FLI1_uc010sbv.1_5'Flank|FLI1_uc009zci.2_5'Flank|uc001qel.2_Intron	NM_002017	NP_002008			Friend leukemia virus integration 1						hemostasis|organ morphogenesis	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		EWSR1/FLI1(2266)	bone(2210)|soft_tissue(48)|autonomic_ganglia(4)|central_nervous_system(4)|lung(3)|ovary(2)|pancreas(2)	2273	all_hematologic(175;0.0641)	Lung NSC(97;0.00588)|all_lung(97;0.00764)|Breast(109;0.0115)|Medulloblastoma(222;0.0523)|all_neural(223;0.0862)|all_hematologic(192;0.182)		OV - Ovarian serous cystadenocarcinoma(99;0.01)|LUSC - Lung squamous cell carcinoma(976;0.0324)|Lung(977;0.0327)				T	EWSR1	Ewing sarcoma								---	---	---	---
FLI1	2313	broad.mit.edu	37	11	128641924	128641935	+	Intron	DEL	CACACACACACA	-	-	rs66765733		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128641924_128641935delCACACACACACA	uc010sbu.1	+						FLI1_uc010sbt.1_Intron|FLI1_uc010sbv.1_Intron|FLI1_uc009zci.2_Intron	NM_002017	NP_002008			Friend leukemia virus integration 1						hemostasis|organ morphogenesis	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		EWSR1/FLI1(2266)	bone(2210)|soft_tissue(48)|autonomic_ganglia(4)|central_nervous_system(4)|lung(3)|ovary(2)|pancreas(2)	2273	all_hematologic(175;0.0641)	Lung NSC(97;0.00588)|all_lung(97;0.00764)|Breast(109;0.0115)|Medulloblastoma(222;0.0523)|all_neural(223;0.0862)|all_hematologic(192;0.182)		OV - Ovarian serous cystadenocarcinoma(99;0.01)|LUSC - Lung squamous cell carcinoma(976;0.0324)|Lung(977;0.0327)				T	EWSR1	Ewing sarcoma								---	---	---	---
ARHGAP32	9743	broad.mit.edu	37	11	128843573	128843573	+	Intron	DEL	A	-	-	rs10893942	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128843573delA	uc009zcp.2	-						ARHGAP32_uc009zcq.1_3'UTR|ARHGAP32_uc009zco.2_5'UTR|ARHGAP32_uc001qez.2_Intron	NM_001142685	NP_001136157			Rho GTPase-activating protein isoform 1						cell communication|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell cortex|cell junction|cytosol|dendritic spine|endoplasmic reticulum membrane|endosome membrane|Golgi membrane|postsynaptic density|postsynaptic membrane	GTPase activator activity|phosphatidylinositol binding			lung(3)|ovary(2)	5																		---	---	---	---
ARHGAP32	9743	broad.mit.edu	37	11	128856290	128856291	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128856290_128856291insT	uc009zcp.2	-						ARHGAP32_uc009zcq.1_Intron|ARHGAP32_uc009zco.2_Intron|ARHGAP32_uc001qez.2_Intron|ARHGAP32_uc001qfb.2_Intron	NM_001142685	NP_001136157			Rho GTPase-activating protein isoform 1						cell communication|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell cortex|cell junction|cytosol|dendritic spine|endoplasmic reticulum membrane|endosome membrane|Golgi membrane|postsynaptic density|postsynaptic membrane	GTPase activator activity|phosphatidylinositol binding			lung(3)|ovary(2)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	129216193	129216193	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129216193delA								ARHGAP32 (154100 upstream) : BARX2 (29688 downstream)																																			---	---	---	---
NFRKB	4798	broad.mit.edu	37	11	129759925	129759925	+	Intron	DEL	T	-	-	rs71899258		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129759925delT	uc001qfi.2	-						NFRKB_uc001qfg.2_Intron|NFRKB_uc001qfh.2_Intron|NFRKB_uc010sbw.1_Intron	NM_001143835	NP_001137307			nuclear factor related to kappaB binding protein						DNA recombination|DNA repair|inflammatory response|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	Ino80 complex	DNA binding|protease binding			ovary(3)	3	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	129889837	129889838	+	IGR	DEL	TG	-	-	rs80341702		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129889837_129889838delTG								NCRNA00167 (14456 upstream) : APLP2 (49878 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	130243141	130243141	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130243141delA	uc001qgd.2	+						uc010scb.1_Intron|uc010scc.1_Intron					Homo sapiens cDNA FLJ34521 fis, clone HLUNG2007041.																														---	---	---	---
NTM	50863	broad.mit.edu	37	11	132145949	132145949	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132145949delT	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|NTM_uc001qgr.2_Intron	NM_016522	NP_057606			neurotrimin isoform 1						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
OPCML	4978	broad.mit.edu	37	11	133184453	133184454	+	Intron	DEL	AA	-	-	rs113865874		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133184453_133184454delAA	uc001qgu.2	-							NM_001012393	NP_001012393			opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	133523820	133523820	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133523820delT								OPCML (121417 upstream) : SPATA19 (186697 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	133554343	133554343	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133554343delA								OPCML (151940 upstream) : SPATA19 (156174 downstream)																																			---	---	---	---
IGSF9B	22997	broad.mit.edu	37	11	133789014	133789014	+	Intron	DEL	G	-	-	rs72000603		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133789014delG	uc001qgx.3	-							NM_014987	NP_055802			immunoglobulin superfamily, member 9B							integral to membrane|plasma membrane					0	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)														---	---	---	---
JAM3	83700	broad.mit.edu	37	11	134021120	134021120	+	3'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134021120delT	uc001qhb.1	+	9					JAM3_uc009zcz.1_3'UTR	NM_032801	NP_116190			junctional adhesion molecule 3 precursor						angiogenesis|blood coagulation|regulation of neutrophil chemotaxis	cell-cell contact zone|desmosome|extracellular space|integral to membrane	integrin binding			ovary(1)	1	all_hematologic(175;0.127)	all_cancers(12;1.06e-21)|all_epithelial(12;3.37e-16)|all_lung(97;7.03e-06)|Lung NSC(97;1.67e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0506)|Esophageal squamous(93;0.0566)		Epithelial(10;1.55e-09)|BRCA - Breast invasive adenocarcinoma(10;1.35e-08)|all cancers(11;2.81e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00402)|Lung(977;0.245)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	134298556	134298565	+	IGR	DEL	CCCTCCTGCT	-	-	rs67272036		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134298556_134298565delCCCTCCTGCT								B3GAT1 (16744 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	66438	66438	+	5'Flank	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66438delC	uc010scw.1	+											Homo sapiens chromosome 6 F379 retina specific protein (F379) mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	169020	169021	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:169020_169021insA								FAM138D (19608 upstream) : IQSEC3 (7182 downstream)																																			---	---	---	---
WNK1	65125	broad.mit.edu	37	12	917666	917667	+	Intron	INS	-	T	T	rs148456638	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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	947244	947245	+	Intron	INS	-	GT	GT	rs143597723	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:947244_947245insGT	uc001qio.3	+						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	1018422	1018422	+	3'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1018422delT	uc001qio.3	+	28					WNK1_uc001qip.3_3'UTR|WNK1_uc001qir.3_3'UTR	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	1035008	1035008	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1035008delT	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					---	---	---	---
RAD52	5893	broad.mit.edu	37	12	1074860	1074860	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1074860delT	uc001qiu.1	-							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	1436057	1436057	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1436057delT	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	1781456	1781456	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1781456delC								WNT5B (25079 upstream) : ADIPOR2 (18791 downstream)																																			---	---	---	---
CACNA1C	775	broad.mit.edu	37	12	2301236	2301237	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2301236_2301237delAC	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)													---	---	---	---
TEAD4	7004	broad.mit.edu	37	12	3065847	3065848	+	5'Flank	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3065847_3065848delTT	uc010sej.1	+						TEAD4_uc010sek.1_5'Flank	NM_003213	NP_003204			TEA domain family member 4 isoform 1						hippo signaling cascade|muscle organ development|skeletal system development		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0	Ovarian(42;0.211)		OV - Ovarian serous cystadenocarcinoma(31;0.000563)|COAD - Colon adenocarcinoma(12;0.0831)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	3179545	3179545	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3179545delT								TEAD4 (29704 upstream) : TSPAN9 (7012 downstream)																																			---	---	---	---
EFCAB4B	84766	broad.mit.edu	37	12	3863424	3863425	+	5'Flank	DEL	TC	-	-	rs10554738		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3863424_3863425delTC	uc001qmj.2	-						EFCAB4B_uc010sen.1_5'Flank|EFCAB4B_uc010seo.1_5'Flank	NM_032680	NP_116069			EF-hand calcium binding domain 4B isoform c						activation of store-operated calcium channel activity|store-operated calcium entry	cytoplasm	calcium ion binding|protein binding			ovary(1)|pancreas(1)	2			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	3902409	3902410	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3902409_3902410delAC								EFCAB4B (40043 upstream) : PARP11 (15617 downstream)																																			---	---	---	---
PARP11	57097	broad.mit.edu	37	12	3930644	3930644	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3930644delT	uc001qmk.1	-						PARP11_uc001qml.2_Intron|PARP11_uc009zef.2_Intron|PARP11_uc001qmm.2_Intron|PARP11_uc001qmn.2_Intron	NM_020367	NP_065100			poly (ADP-ribose) polymerase family, member 11								NAD+ ADP-ribosyltransferase activity			ovary(1)|central_nervous_system(1)	2			all cancers(3;1.58e-07)|OV - Ovarian serous cystadenocarcinoma(31;0.00287)|GBM - Glioblastoma multiforme(3;0.0141)|COAD - Colon adenocarcinoma(12;0.0264)															---	---	---	---
CCND2	894	broad.mit.edu	37	12	4398350	4398350	+	Intron	DEL	G	-	-	rs78692066		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4398350delG	uc001qmo.2	+							NM_001759	NP_001750			cyclin D2						cell division|positive regulation of cyclin-dependent protein kinase activity|positive regulation of protein phosphorylation	cyclin-dependent protein kinase holoenzyme complex|cytoplasm|membrane|nucleus	protein kinase binding			haematopoietic_and_lymphoid_tissue(1)|breast(1)|kidney(1)	3			all cancers(3;4.15e-10)|GBM - Glioblastoma multiforme(3;6.34e-05)|Colorectal(7;0.00245)|OV - Ovarian serous cystadenocarcinoma(31;0.00301)|COAD - Colon adenocarcinoma(12;0.0264)|STAD - Stomach adenocarcinoma(119;0.206)					T	IGL@	NHL,CLL								---	---	---	---
Unknown	0	broad.mit.edu	37	12	4563617	4563617	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4563617delA								FGF6 (8837 upstream) : C12orf4 (33294 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	4573994	4573994	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4573994delA								FGF6 (19214 upstream) : C12orf4 (22917 downstream)																																			---	---	---	---
DYRK4	8798	broad.mit.edu	37	12	4723002	4723002	+	3'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4723002delT	uc001qmx.2	+	13					DYRK4_uc001qmy.1_3'UTR|DYRK4_uc001qmz.1_3'UTR|DYRK4_uc001qna.1_3'UTR|DYRK4_uc010ser.1_3'UTR	NM_003845	NP_003836			dual-specificity tyrosine-(Y)-phosphorylation							Golgi apparatus	ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(2)|skin(1)	3			Colorectal(7;0.103)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	5103770	5103770	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5103770delG								KCNA1 (76350 upstream) : KCNA5 (49315 downstream)																																			---	---	---	---
VWF	7450	broad.mit.edu	37	12	6126787	6126787	+	Intron	DEL	T	-	-	rs67100831		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6126787delT	uc001qnn.1	-						VWF_uc010set.1_Intron	NM_000552	NP_000543			von Willebrand factor preproprotein						blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)													---	---	---	---
VWF	7450	broad.mit.edu	37	12	6167292	6167292	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6167292delA	uc001qnn.1	-						VWF_uc010set.1_Intron	NM_000552	NP_000543			von Willebrand factor preproprotein						blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	6282321	6282321	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6282321delC								VWF (48485 upstream) : CD9 (26552 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	6284329	6284329	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6284329delA								VWF (50493 upstream) : CD9 (24544 downstream)																																			---	---	---	---
CHD4	1108	broad.mit.edu	37	12	6690187	6690187	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6690187delA	uc001qpo.2	-						CHD4_uc001qpn.2_Intron|CHD4_uc001qpp.2_Intron|uc001qpq.1_Intron	NM_001273	NP_001264			chromodomain helicase DNA binding protein 4						chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|DNA binding|zinc ion binding			central_nervous_system(2)	2																		---	---	---	---
C12orf53	196500	broad.mit.edu	37	12	6806716	6806716	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6806716delG	uc001qqf.1	-	3	336	c.260delC	c.(259-261)CCAfs	p.P87fs	C12orf53_uc001qqg.1_Frame_Shift_Del_p.P87fs	NM_153685	NP_710152	Q8IYJ0	CL053_HUMAN	hypothetical protein LOC196500 precursor	87	Extracellular (Potential).					integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	6893761	6893761	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6893761delA								LAG3 (6142 upstream) : CD4 (4890 downstream)																																			---	---	---	---
C1S	716	broad.mit.edu	37	12	7116392	7116392	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7116392delT	uc001qsj.2	+						LPCAT3_uc010sfw.1_Intron|LPCAT3_uc001qsi.2_Intron|LPCAT3_uc009zfp.2_Intron|LPCAT3_uc010sfx.1_Intron|LPCAT3_uc009zfq.1_Intron	NM_201442	NP_958850			complement component 1, s subcomponent						complement activation, classical pathway|innate immune response|proteolysis	extracellular region	calcium ion binding|serine-type endopeptidase activity			skin(1)	1					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	7719747	7719747	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7719747delA								CD163 (63333 upstream) : APOBEC1 (82250 downstream)																																			---	---	---	---
SLC2A14	144195	broad.mit.edu	37	12	7982151	7982151	+	Intron	DEL	A	-	-	rs36068117		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7982151delA	uc001qtk.2	-						SLC2A14_uc001qtl.2_Intron|SLC2A14_uc001qtm.2_Intron|SLC2A14_uc010sgg.1_Intron|SLC2A14_uc001qtn.2_Intron|SLC2A14_uc001qto.2_Intron|SLC2A14_uc010sgh.1_Intron	NM_153449	NP_703150			glucose transporter 14						cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane	glucose transmembrane transporter activity			ovary(1)	1				Kidney(36;0.0883)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	8095541	8095541	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8095541delT								SLC2A3 (6649 upstream) : FOXJ2 (89818 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	8098518	8098519	+	IGR	INS	-	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8098518_8098519insG								SLC2A3 (9626 upstream) : FOXJ2 (86840 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	8267357	8267357	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8267357delT								NECAP1 (16984 upstream) : CLEC4A (8871 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	8603688	8603688	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8603688delA								LOC389634 (54289 upstream) : CLEC6A (4903 downstream)																																			---	---	---	---
RIMKLB	57494	broad.mit.edu	37	12	8854024	8854024	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8854024delT	uc001quu.2	+						RIMKLB_uc009zgf.1_Intron|RIMKLB_uc001qux.2_Intron|RIMKLB_uc010sgl.1_Intron|RIMKLB_uc001quw.2_Intron	NM_020734	NP_065785			ribosomal modification protein rimK-like family						protein modification process	cytoplasm	acid-amino acid ligase activity|ATP binding|metal ion binding				0																		---	---	---	---
RIMKLB	57494	broad.mit.edu	37	12	8906367	8906367	+	Intron	DEL	A	-	-	rs146605560		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8906367delA	uc001quu.2	+						RIMKLB_uc009zgf.1_Intron|RIMKLB_uc001qux.2_Intron|RIMKLB_uc010sgl.1_Intron|RIMKLB_uc001quw.2_Intron	NM_020734	NP_065785			ribosomal modification protein rimK-like family						protein modification process	cytoplasm	acid-amino acid ligase activity|ATP binding|metal ion binding				0																		---	---	---	---
A2ML1	144568	broad.mit.edu	37	12	9004010	9004011	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9004010_9004011delTT	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																		---	---	---	---
OLR1	4973	broad.mit.edu	37	12	10319126	10319126	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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																		---	---	---	---
KLRA1	10748	broad.mit.edu	37	12	10750170	10750171	+	Intron	DEL	GA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10750170_10750171delGA	uc010shf.1	-						KLRA1_uc010shg.1_Intron|KLRA1_uc009zho.2_Intron|KLRA1_uc009zhn.2_Intron	NM_006611				Homo sapiens Ly-49L (LY49L) mRNA, complete cds.												0																		---	---	---	---
PRB4	5545	broad.mit.edu	37	12	11045110	11045111	+	Intron	INS	-	GAAAG	GAAAG	rs143138719	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11045110_11045111insGAAAG	uc001qzf.1	-						PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron	NM_002723	NP_002714			proline-rich protein BstNI subfamily 4							extracellular region				ovary(1)	1															HNSCC(22;0.051)			---	---	---	---
PRB4	5545	broad.mit.edu	37	12	11109683	11109683	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11109683delA	uc001qzf.1	-						PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRH1_uc001qzj.2_Intron	NM_002723	NP_002714			proline-rich protein BstNI subfamily 4							extracellular region				ovary(1)	1															HNSCC(22;0.051)			---	---	---	---
PRB4	5545	broad.mit.edu	37	12	11192122	11192123	+	Intron	INS	-	T	T	rs146658463	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11192122_11192123insT	uc001qzf.1	-						PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRH1_uc001qzj.2_Intron	NM_002723	NP_002714			proline-rich protein BstNI subfamily 4							extracellular region				ovary(1)	1															HNSCC(22;0.051)			---	---	---	---
PRB4	5545	broad.mit.edu	37	12	11358619	11358619	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11358619delA	uc001qzf.1	-							NM_002723	NP_002714			proline-rich protein BstNI subfamily 4							extracellular region				ovary(1)	1															HNSCC(22;0.051)			---	---	---	---
LRP6	4040	broad.mit.edu	37	12	12327053	12327053	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12327053delT	uc001rah.3	-						BCL2L14_uc001raf.1_Intron|LRP6_uc010shl.1_Intron	NM_002336	NP_002327			low density lipoprotein receptor-related protein						cellular response to cholesterol|negative regulation of protein phosphorylation|negative regulation of protein serine/threonine kinase activity|negative regulation of smooth muscle cell apoptosis|neural crest formation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell cycle|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	cell surface|cytoplasmic vesicle|endoplasmic reticulum|integral to membrane|plasma membrane	coreceptor activity|frizzled binding|kinase inhibitor activity|low-density lipoprotein receptor activity|protein homodimerization activity|toxin transporter activity|Wnt-protein binding			lung(4)|skin(4)|ovary(2)|kidney(1)|central_nervous_system(1)	12		Prostate(47;0.0865)																---	---	---	---
LRP6	4040	broad.mit.edu	37	12	12408238	12408241	+	Intron	DEL	AAAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12408238_12408241delAAAA	uc001rah.3	-						LRP6_uc010shl.1_Intron	NM_002336	NP_002327			low density lipoprotein receptor-related protein						cellular response to cholesterol|negative regulation of protein phosphorylation|negative regulation of protein serine/threonine kinase activity|negative regulation of smooth muscle cell apoptosis|neural crest formation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell cycle|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	cell surface|cytoplasmic vesicle|endoplasmic reticulum|integral to membrane|plasma membrane	coreceptor activity|frizzled binding|kinase inhibitor activity|low-density lipoprotein receptor activity|protein homodimerization activity|toxin transporter activity|Wnt-protein binding			lung(4)|skin(4)|ovary(2)|kidney(1)|central_nervous_system(1)	12		Prostate(47;0.0865)																---	---	---	---
LOH12CR1	118426	broad.mit.edu	37	12	12532052	12532053	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12532052_12532053delTT	uc001ral.2	+						LOH12CR1_uc009zhu.2_Intron	NM_058169	NP_477517			LOH1CR12											ovary(1)	1		Prostate(47;0.0802)		BRCA - Breast invasive adenocarcinoma(232;0.0205)														---	---	---	---
LOH12CR1	118426	broad.mit.edu	37	12	12610591	12610592	+	Intron	INS	-	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12610591_12610592insC	uc001ral.2	+						LOH12CR1_uc009zhu.2_Intron	NM_058169	NP_477517			LOH1CR12											ovary(1)	1		Prostate(47;0.0802)		BRCA - Breast invasive adenocarcinoma(232;0.0205)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	12864225	12864228	+	IGR	DEL	AAAA	-	-	rs34678069		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12864225_12864228delAAAA								GPR19 (15104 upstream) : CDKN1B (6074 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	14492266	14492266	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14492266delA								GRIN2B (359244 upstream) : ATF7IP (26345 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	14509449	14509449	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14509449delT								GRIN2B (376427 upstream) : ATF7IP (9162 downstream)																																			---	---	---	---
PLBD1	79887	broad.mit.edu	37	12	14656992	14656992	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14656992delT	uc001rcc.1	-							NM_024829	NP_079105			phospholipase B domain containing 1						lipid catabolic process	extracellular region	hydrolase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	15454165	15454165	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15454165delA								RERG (79861 upstream) : PTPRO (21322 downstream)																																			---	---	---	---
PTPRO	5800	broad.mit.edu	37	12	15633656	15633671	+	Intron	DEL	GATGGATGGATGGATG	-	-	rs72315531		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15633656_15633671delGATGGATGGATGGATG	uc001rcv.1	+						PTPRO_uc001rcw.1_Intron|PTPRO_uc001rcu.1_Intron	NM_030667	NP_109592			receptor-type protein tyrosine phosphatase O							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	9		Hepatocellular(102;0.244)																---	---	---	---
Unknown	0	broad.mit.edu	37	12	16259072	16259074	+	IGR	DEL	TTT	-	-	rs79003612		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16259072_16259074delTTT								DERA (68758 upstream) : MGST1 (241002 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	16413987	16413987	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16413987delT								DERA (223673 upstream) : MGST1 (86089 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	16448963	16448964	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16448963_16448964delAC								DERA (258649 upstream) : MGST1 (51112 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	16614998	16614998	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16614998delA								MGST1 (91656 upstream) : LMO3 (86309 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	16842820	16842823	+	IGR	DEL	TTAT	-	-	rs12318529		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16842820_16842823delTTAT								LMO3 (80062 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	16879311	16879314	+	IGR	DEL	TTCC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16879311_16879314delTTCC								LMO3 (116553 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	16887526	16887526	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16887526delA								LMO3 (124768 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	17660146	17660147	+	IGR	DEL	GT	-	-	rs35942031		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:17660146_17660147delGT								LMO3 (897388 upstream) : RERGL (573657 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	17829045	17829045	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:17829045delG								None (None upstream) : RERGL (404759 downstream)																																			---	---	---	---
PLEKHA5	54477	broad.mit.edu	37	12	19516768	19516768	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19516768delA	uc001reb.2	+						PLEKHA5_uc001rea.2_Intron|PLEKHA5_uc009zin.2_Intron|PLEKHA5_uc010sif.1_Intron|PLEKHA5_uc010sig.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	19775210	19775210	+	IGR	DEL	A	-	-	rs76677371		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19775210delA								AEBP2 (100037 upstream) : PDE3A (746987 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	19867686	19867686	+	IGR	DEL	T	-	-	rs113689405		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19867686delT								AEBP2 (192513 upstream) : PDE3A (654511 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	19913757	19913757	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19913757delC								AEBP2 (238584 upstream) : PDE3A (608440 downstream)																																			---	---	---	---
PDE3A	5139	broad.mit.edu	37	12	20828993	20828994	+	Intron	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20828993_20828994delTC	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)													---	---	---	---
SLCO1C1	53919	broad.mit.edu	37	12	20892276	20892276	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20892276delA	uc001rej.3	+						SLCO1C1_uc010sii.1_Intron|SLCO1C1_uc010sij.1_Intron|SLCO1C1_uc009zip.2_Intron|SLCO1C1_uc001rei.2_Intron|SLCO1C1_uc010sik.1_Intron	NM_017435	NP_059131			solute carrier organic anion transporter family,						sodium-independent organic anion transport	integral to membrane|plasma membrane	thyroid hormone transmembrane transporter activity			ovary(5)|pancreas(1)|skin(1)	7	Esophageal squamous(101;0.149)																	---	---	---	---
SLCO1C1	53919	broad.mit.edu	37	12	20894585	20894585	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20894585delT	uc001rej.3	+						SLCO1C1_uc010sii.1_Intron|SLCO1C1_uc010sij.1_Intron|SLCO1C1_uc009zip.2_Intron|SLCO1C1_uc001rei.2_Intron|SLCO1C1_uc010sik.1_Intron	NM_017435	NP_059131			solute carrier organic anion transporter family,						sodium-independent organic anion transport	integral to membrane|plasma membrane	thyroid hormone transmembrane transporter activity			ovary(5)|pancreas(1)|skin(1)	7	Esophageal squamous(101;0.149)																	---	---	---	---
SLCO1B3	28234	broad.mit.edu	37	12	20969512	20969512	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20969512delT	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	21182794	21182794	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21182794delT	uc010sil.1	+						LST-3TM12_uc010sim.1_Intron|LST-3TM12_uc010sin.1_Intron					SubName: Full=Liver-specific organic anion transporter 3TM13; SubName: Full=Organic anion transporter LST-3c;						bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|cytoplasm|integral to plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(2)|ovary(1)|skin(1)	4	Esophageal squamous(101;0.149)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	21251778	21251778	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21251778delT								SLCO1B3 (8740 upstream) : SLCO1B1 (32350 downstream)																																			---	---	---	---
SLCO1A2	6579	broad.mit.edu	37	12	21499908	21499909	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21499908_21499909delAA	uc001res.2	-						SLCO1A2_uc010siq.1_Intron	NM_134431	NP_602307			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																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	21900148	21900148	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21900148delA								LDHB (89372 upstream) : KCNJ8 (17742 downstream)																																			---	---	---	---
ABCC9	10060	broad.mit.edu	37	12	22025423	22025423	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22025423delT	uc001rfi.1	-						ABCC9_uc001rfh.2_Intron|ABCC9_uc001rfj.1_Intron	NM_005691	NP_005682			ATP-binding cassette, sub-family C, member 9						defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)|skin(2)	6					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)													---	---	---	---
ETNK1	55500	broad.mit.edu	37	12	22796337	22796338	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22796337_22796338delAC	uc001rft.2	+						ETNK1_uc009ziz.2_Intron|ETNK1_uc001rfs.2_Intron	NM_018638	NP_061108			ethanolamine kinase 1 isoform A						phosphatidylethanolamine biosynthetic process	cytoplasm	ATP binding|ethanolamine kinase activity				0																		---	---	---	---
ETNK1	55500	broad.mit.edu	37	12	22816785	22816785	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22816785delT	uc001rft.2	+						ETNK1_uc009ziz.2_Intron	NM_018638	NP_061108			ethanolamine kinase 1 isoform A						phosphatidylethanolamine biosynthetic process	cytoplasm	ATP binding|ethanolamine kinase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	22912907	22912907	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22912907delA								ETNK1 (69300 upstream) : SOX5 (772325 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	22995210	22995215	+	IGR	DEL	TTTTTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22995210_22995215delTTTTTT								ETNK1 (151603 upstream) : SOX5 (690017 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	23203317	23203318	+	Intron	INS	-	TCATATCT	TCATATCT	rs147857519	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:23203317_23203318insTCATATCT	uc001rfu.1	+											Homo sapiens cDNA FLJ37414 fis, clone BRAWH1000157.																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	23481140	23481140	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:23481140delA								ETNK1 (637533 upstream) : SOX5 (204092 downstream)																																			---	---	---	---
SOX5	6660	broad.mit.edu	37	12	24129752	24129752	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:24129752delT	uc001rfx.2	-						SOX5_uc001rfy.2_Intron	NM_152989	NP_694534			SRY (sex determining region Y)-box 5 isoform b						transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(5)|lung(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	24958123	24958123	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:24958123delA								SOX5 (242743 upstream) : BCAT1 (6158 downstream)																																			---	---	---	---
BCAT1	586	broad.mit.edu	37	12	25004919	25004919	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25004919delG	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)													---	---	---	---
KRAS	3845	broad.mit.edu	37	12	25368594	25368594	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25368594delT	uc001rgp.1	-						KRAS_uc001rgq.1_Intron	NM_033360	NP_203524			c-K-ras2 protein isoform a precursor						activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	plasma membrane	GTP binding|GTPase activity|protein binding			large_intestine(12391)|pancreas(3285)|lung(2847)|biliary_tract(521)|ovary(443)|endometrium(339)|haematopoietic_and_lymphoid_tissue(318)|stomach(203)|thyroid(149)|prostate(85)|soft_tissue(77)|small_intestine(62)|upper_aerodigestive_tract(59)|cervix(49)|urinary_tract(48)|skin(38)|liver(31)|breast(28)|testis(17)|oesophagus(15)|central_nervous_system(9)|peritoneum(6)|salivary_gland(6)|kidney(5)|gastrointestinal_tract_(site_indeterminate)(5)|thymus(5)|eye(4)|autonomic_ganglia(2)|bone(2)|genital_tract(1)|penis(1)|adrenal_gland(1)	21052	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)				119	Mis		pancreatic|colorectal|lung|thyroid|AML|others				Cardiofaciocutaneous_syndrome|Noonan_syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			---	---	---	---
Unknown	0	broad.mit.edu	37	12	25996903	25996903	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25996903delA								IFLTD1 (195415 upstream) : RASSF8 (115066 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	26446481	26446483	+	IGR	DEL	GAA	-	-	rs79148752		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26446481_26446483delGAA								SSPN (40628 upstream) : ITPR2 (41804 downstream)																																			---	---	---	---
ITPR2	3709	broad.mit.edu	37	12	26902792	26902792	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26902792delT	uc001rhg.2	-						ITPR2_uc001rhh.1_Intron|ITPR2_uc001rhi.1_Intron	NM_002223	NP_002214			inositol 1,4,5-triphosphate receptor, type 2						activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)																	---	---	---	---
TM7SF3	51768	broad.mit.edu	37	12	27133722	27133722	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27133722delA	uc010sjl.1	-							NM_016551	NP_057635			transmembrane 7 superfamily member 3 precursor							integral to membrane|plasma membrane				upper_aerodigestive_tract(2)	2	Colorectal(261;0.0847)																	---	---	---	---
ARNTL2	56938	broad.mit.edu	37	12	27506625	27506625	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27506625delC	uc001rht.1	+						ARNTL2_uc001rhw.2_Intron|ARNTL2_uc010sjp.1_Intron|ARNTL2_uc001rhu.1_Intron|ARNTL2_uc009zji.1_Intron|ARNTL2_uc001rhv.1_Intron	NM_020183	NP_064568			aryl hydrocarbon receptor nuclear						circadian rhythm|entrainment of circadian clock|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(1)|skin(1)	2	Colorectal(261;0.0847)|Lung SC(9;0.184)																	---	---	---	---
C12orf70	341346	broad.mit.edu	37	12	27641990	27641990	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27641990delT	uc010sjq.1	+							NM_001145010	NP_001138482			hypothetical protein LOC341346							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	28133543	28133543	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28133543delA								PTHLH (8627 upstream) : CCDC91 (198667 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	28200703	28200705	+	IGR	DEL	CAA	-	-	rs67149920		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28200703_28200705delCAA								PTHLH (75787 upstream) : CCDC91 (131505 downstream)																																			---	---	---	---
CCDC91	55297	broad.mit.edu	37	12	28447524	28447524	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28447524delT	uc001riq.2	+						CCDC91_uc001rio.2_Intron|CCDC91_uc009zjk.2_Intron|CCDC91_uc001rip.1_Intron	NM_018318	NP_060788			GGA binding partner						protein transport	Golgi apparatus|membrane				central_nervous_system(1)	1	Acute lymphoblastic leukemia(23;0.00718)|all_hematologic(23;0.0113)|Lung SC(9;0.184)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	28720579	28720580	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28720579_28720580insA								CCDC91 (17481 upstream) : FAR2 (581652 downstream)																																			---	---	---	---
TMTC1	83857	broad.mit.edu	37	12	29765337	29765337	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29765337delT	uc001rjb.2	-						TMTC1_uc001riz.2_Intron|TMTC1_uc001rja.2_Intron|TMTC1_uc001rjc.1_Intron	NM_175861	NP_787057			transmembrane and tetratricopeptide repeat							integral to membrane	binding				0	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)																	---	---	---	---
TMTC1	83857	broad.mit.edu	37	12	29835421	29835421	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29835421delA	uc001rjb.2	-						TMTC1_uc001rja.2_Intron|TMTC1_uc001rjc.1_Intron	NM_175861	NP_787057			transmembrane and tetratricopeptide repeat							integral to membrane	binding				0	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)																	---	---	---	---
TMTC1	83857	broad.mit.edu	37	12	29925292	29925293	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29925292_29925293insT	uc001rjb.2	-						TMTC1_uc001rjc.1_Intron	NM_175861	NP_787057			transmembrane and tetratricopeptide repeat							integral to membrane	binding				0	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)																	---	---	---	---
FAM60A	58516	broad.mit.edu	37	12	31435557	31435557	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31435557delA	uc010sjz.1	-	6					FAM60A_uc001rkd.2_3'UTR|FAM60A_uc010ska.1_3'UTR|FAM60A_uc001rke.2_3'UTR|FAM60A_uc010skb.1_RNA|FAM60A_uc001rkc.2_3'UTR	NM_021238	NP_067061			family with sequence similarity 60, member A												0	all_cancers(9;5.22e-13)|all_epithelial(9;4e-13)|all_lung(12;1.2e-11)|Lung NSC(12;2.17e-09)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0207)|Lung SC(12;0.0592)|Esophageal squamous(101;0.162)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	31762829	31762829	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31762829delC								DENND5B (18877 upstream) : C12orf72 (37265 downstream)																																			---	---	---	---
AMN1	196394	broad.mit.edu	37	12	31858426	31858426	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31858426delA	uc001rkq.3	-						AMN1_uc001rko.3_Intron|AMN1_uc010skc.1_Intron|AMN1_uc001rkp.3_Intron|AMN1_uc009zjs.2_Intron|AMN1_uc009zjt.1_Intron	NM_001113402	NP_001106873			antagonist of mitotic exit network 1 homolog												0	all_cancers(9;7.41e-12)|all_epithelial(9;1.18e-11)|all_lung(12;1.14e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0336)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.162)		OV - Ovarian serous cystadenocarcinoma(6;0.0014)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	31926211	31926211	+	IGR	DEL	A	-	-	rs7956226	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31926211delA								AMN1 (44103 upstream) : H3F3C (17910 downstream)																																			---	---	---	---
DNM1L	10059	broad.mit.edu	37	12	32837412	32837412	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32837412delT	uc001rld.2	+						DNM1L_uc010skf.1_Intron|DNM1L_uc010skg.1_Intron|DNM1L_uc001rle.2_Intron|DNM1L_uc001rlf.2_Intron|DNM1L_uc010skh.1_Intron|DNM1L_uc001rlg.2_Intron|DNM1L_uc001rlh.2_Intron|DNM1L_uc010ski.1_Intron	NM_012062	NP_036192			dynamin 1-like isoform 1						cellular component disassembly involved in apoptosis|mitochondrial fragmentation involved in apoptosis|mitochondrial membrane organization|positive regulation of mitochondrial fission	cis-Golgi network|cytosol|endomembrane system|endoplasmic reticulum|mitochondrial outer membrane	GTP binding|GTPase activity|ubiquitin protein ligase binding			ovary(1)|pancreas(1)	2	Lung NSC(5;2.15e-06)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	33653944	33653944	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:33653944delT								SYT10 (61190 upstream) : ALG10 (521272 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	33698579	33698579	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:33698579delT								SYT10 (105825 upstream) : ALG10 (476637 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	33707351	33707351	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:33707351delT								SYT10 (114597 upstream) : ALG10 (467865 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	33760508	33760509	+	IGR	INS	-	TT	TT	rs151329350	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:33760508_33760509insTT								SYT10 (167754 upstream) : ALG10 (414707 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	34102508	34102509	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34102508_34102509delTT								SYT10 (509754 upstream) : ALG10 (72707 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	34477443	34477443	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34477443delT								ALG10 (296209 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	34835146	34835146	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34835146delT								ALG10 (653912 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	37938173	37938174	+	IGR	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:37938173_37938174delGT								None (None upstream) : ALG10B (772383 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	38514735	38514736	+	IGR	DEL	TT	-	-	rs34841181		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38514735_38514736delTT								None (None upstream) : ALG10B (195821 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	40524267	40524267	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40524267delT								SLC2A13 (24606 upstream) : LRRK2 (94546 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	40963212	40963212	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40963212delT	uc001rml.1	+											Homo sapiens cDNA FLJ35746 fis, clone TESTI2004399, moderately similar to APOMUCIN.																														---	---	---	---
CNTN1	1272	broad.mit.edu	37	12	41404668	41404668	+	Intron	DEL	T	-	-	rs35933164		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41404668delT	uc001rmm.1	+						CNTN1_uc001rmn.1_Intron	NM_001843	NP_001834			contactin 1 isoform 1 precursor						axon guidance|cell adhesion|Notch signaling pathway	anchored to membrane|membrane fraction|plasma membrane				lung(4)|ovary(3)|large_intestine(1)|skin(1)	9	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)																---	---	---	---
GXYLT1	283464	broad.mit.edu	37	12	42486662	42486662	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42486662delA	uc001rms.3	-						GXYLT1_uc001rmt.3_Intron	NM_173601	NP_775872			glycosyltransferase 8 domain containing 3						O-glycan processing	integral to membrane	UDP-xylosyltransferase activity				0																		---	---	---	---
PPHLN1	51535	broad.mit.edu	37	12	42664476	42664477	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42664476_42664477delAA	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	42857123	42857123	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42857123delA	uc010skv.1	-						PRICKLE1_uc001rnl.2_Intron|PRICKLE1_uc010skw.1_Intron|PRICKLE1_uc001rnm.2_Intron	NM_001144881	NP_001138353			prickle homolog 1						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cardiac muscle cell myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein import into nucleus	cytosol|nuclear membrane	zinc ion binding			ovary(3)|skin(1)	4	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	43262197	43262197	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43262197delT								PRICKLE1 (278625 upstream) : ADAMTS20 (485816 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	43412075	43412075	+	IGR	DEL	A	-	-	rs36089311		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43412075delA								PRICKLE1 (428503 upstream) : ADAMTS20 (335938 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	43415094	43415095	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43415094_43415095delTC								PRICKLE1 (431522 upstream) : ADAMTS20 (332918 downstream)																																			---	---	---	---
IRAK4	51135	broad.mit.edu	37	12	44177446	44177447	+	Intron	INS	-	T	T	rs11182263	by1000genomes;by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44177446_44177447insT	uc001rnu.3	+						IRAK4_uc001rnt.3_Intron|IRAK4_uc001rnx.3_Intron|IRAK4_uc001rny.3_Intron|IRAK4_uc010sky.1_Intron|IRAK4_uc001rnv.3_Intron|IRAK4_uc001rnw.3_Intron	NM_001114182	NP_001107654			interleukin-1 receptor-associated kinase 4						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|endosome membrane|plasma membrane	ATP binding|magnesium ion binding|protein serine/threonine kinase activity				0	all_cancers(12;0.00149)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.04)														---	---	---	---
TMEM117	84216	broad.mit.edu	37	12	44450552	44450553	+	Intron	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44450552_44450553delTC	uc001rod.2	+						TMEM117_uc001roe.2_Intron|TMEM117_uc009zkc.2_Intron	NM_032256	NP_115632			transmembrane protein 117							endoplasmic reticulum|integral to membrane					0	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.124)														---	---	---	---
DBX2	440097	broad.mit.edu	37	12	45412951	45412951	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45412951delA	uc001rok.1	-							NM_001004329	NP_001004329			developing brain homeobox 2							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	Lung SC(27;0.192)	Lung NSC(34;0.142)		GBM - Glioblastoma multiforme(48;0.0515)														---	---	---	---
DBX2	440097	broad.mit.edu	37	12	45427911	45427912	+	Intron	INS	-	CA	CA	rs141193526	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45427911_45427912insCA	uc001rok.1	-							NM_001004329	NP_001004329			developing brain homeobox 2							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	Lung SC(27;0.192)	Lung NSC(34;0.142)		GBM - Glioblastoma multiforme(48;0.0515)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	45485194	45485195	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45485194_45485195delTT								RACGAP1P (26000 upstream) : PLEKHA9 (81652 downstream)																																			---	---	---	---
ARID2	196528	broad.mit.edu	37	12	46211715	46211715	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46211715delT	uc001ros.1	+						ARID2_uc001ror.2_Intron	NM_152641	NP_689854			AT rich interactive domain 2 (ARID, RFX-like)						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(6)|skin(3)|upper_aerodigestive_tract(1)	10	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)														---	---	---	---
ARID2	196528	broad.mit.edu	37	12	46219654	46219655	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46219654_46219655delAA	uc001ros.1	+						ARID2_uc001ror.2_Intron	NM_152641	NP_689854			AT rich interactive domain 2 (ARID, RFX-like)						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(6)|skin(3)|upper_aerodigestive_tract(1)	10	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)														---	---	---	---
ARID2	196528	broad.mit.edu	37	12	46275603	46275603	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46275603delT	uc001ros.1	+						ARID2_uc001ror.2_Intron|ARID2_uc009zkg.1_Intron|ARID2_uc009zkh.1_Intron|ARID2_uc001rou.1_Intron	NM_152641	NP_689854			AT rich interactive domain 2 (ARID, RFX-like)						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(6)|skin(3)|upper_aerodigestive_tract(1)	10	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)														---	---	---	---
SFRS2IP	9169	broad.mit.edu	37	12	46379870	46379870	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46379870delT	uc001rox.2	-						SFRS2IP_uc001roy.1_Intron|SFRS2IP_uc009zki.1_Intron|SFRS2IP_uc001roz.2_Intron	NM_004719	NP_004710			splicing factor, arginine/serine-rich 2,						spliceosome assembly	nucleus	protein binding|zinc ion binding				0	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.209)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.1)														---	---	---	---
FAM113B	91523	broad.mit.edu	37	12	47599556	47599556	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47599556delA	uc001rpn.2	+							NM_138371	NP_612380			hypothetical protein LOC91523								hydrolase activity			skin(3)|ovary(2)	5	Renal(347;0.138)|Lung SC(27;0.192)																	---	---	---	---
RPAP3	79657	broad.mit.edu	37	12	48073181	48073181	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48073181delA	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)																	---	---	---	---
RPAP3	79657	broad.mit.edu	37	12	48095398	48095398	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48095398delA	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	48605535	48605535	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48605535delT								OR10AD1 (8460 upstream) : H1FNT (117228 downstream)																																			---	---	---	---
LALBA	3906	broad.mit.edu	37	12	48963167	48963167	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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																		---	---	---	---
CCNT1	904	broad.mit.edu	37	12	49099496	49099496	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49099496delA	uc001rse.1	-						CCNT1_uc009zkz.1_Intron	NM_001240	NP_001231			cyclin T1						cell cycle|cell division|interspecies interaction between organisms|positive regulation of viral transcription|protein phosphorylation|regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	DNA binding|protein kinase binding			ovary(3)|lung(1)|breast(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	49268229	49268231	+	IGR	DEL	AAA	-	-	rs11419435		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49268229_49268231delAAA								RND1 (8576 upstream) : CCDC65 (29662 downstream)																																			---	---	---	---
PRKAG1	5571	broad.mit.edu	37	12	49406769	49406770	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49406769_49406770insA	uc001rsy.2	-						uc001rsw.2_Intron|PRKAG1_uc010smd.1_Intron|PRKAG1_uc001rsx.2_Intron|PRKAG1_uc001rsz.2_Intron|PRKAG1_uc009zlb.2_Intron|PRKAG1_uc010sme.1_Intron	NM_002733	NP_002724			AMP-activated protein kinase, noncatalytic						cell cycle arrest|fatty acid biosynthetic process|insulin receptor signaling pathway|positive regulation of protein kinase activity|regulation of fatty acid oxidation|regulation of glycolysis|spermatogenesis	cytosol	cAMP-dependent protein kinase activity|cAMP-dependent protein kinase regulator activity|protein kinase binding			kidney(1)	1																		---	---	---	---
PRKAG1	5571	broad.mit.edu	37	12	49410992	49410992	+	Intron	DEL	T	-	-	rs72383476		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49410992delT	uc001rsy.2	-						uc001rsw.2_Intron|PRKAG1_uc010smd.1_Intron|PRKAG1_uc001rsx.2_Intron|PRKAG1_uc001rsz.2_Intron|PRKAG1_uc009zlb.2_Intron|PRKAG1_uc010sme.1_Intron	NM_002733	NP_002724			AMP-activated protein kinase, noncatalytic						cell cycle arrest|fatty acid biosynthetic process|insulin receptor signaling pathway|positive regulation of protein kinase activity|regulation of fatty acid oxidation|regulation of glycolysis|spermatogenesis	cytosol	cAMP-dependent protein kinase activity|cAMP-dependent protein kinase regulator activity|protein kinase binding			kidney(1)	1																		---	---	---	---
MLL2	8085	broad.mit.edu	37	12	49421242	49421242	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49421242delT	uc001rta.3	-							NM_003482	NP_003473			myeloid/lymphoid or mixed-lineage leukemia 2						chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41								N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			---	---	---	---
Unknown	0	broad.mit.edu	37	12	49480976	49480977	+	IGR	DEL	TT	-	-	rs71439489		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49480976_49480977delTT								RHEBL1 (17201 upstream) : DHH (2231 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	49591278	49591278	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49591278delA								TUBA1A (8417 upstream) : TUBA1C (30431 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	49598929	49598929	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49598929delT								TUBA1A (16068 upstream) : TUBA1C (22780 downstream)																																			---	---	---	---
TUBA1C	84790	broad.mit.edu	37	12	49640451	49640451	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49640451delA	uc010smh.1	+						TUBA1C_uc001rts.2_Intron	NM_032704	NP_116093			tubulin alpha 6						'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|protein binding|structural molecule activity				0																		---	---	---	---
SPATS2	65244	broad.mit.edu	37	12	49784861	49784861	+	Intron	DEL	A	-	-	rs72303099		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49784861delA	uc001rud.2	+						SPATS2_uc001ruc.2_Intron|SPATS2_uc001rue.2_Intron|SPATS2_uc009zli.1_Intron|SPATS2_uc001ruf.2_Intron	NM_023071	NP_075559			spermatogenesis associated, serine-rich 2							cytoplasm				breast(1)	1																		---	---	---	---
KCNH3	23416	broad.mit.edu	37	12	49937394	49937394	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49937394delC	uc001ruh.1	+						KCNH3_uc010smj.1_Intron	NM_012284	NP_036416			potassium voltage-gated channel, subfamily H						regulation of transcription, DNA-dependent	integral to membrane	two-component sensor activity|voltage-gated potassium channel activity				0																		---	---	---	---
ACCN2	41	broad.mit.edu	37	12	50470250	50470251	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50470250_50470251delAA	uc001rvw.2	+						ACCN2_uc001rvv.2_Intron|ACCN2_uc009zln.2_Intron|ACCN2_uc009zlo.2_Intron	NM_001095	NP_001086			amiloride-sensitive cation channel 2, neuronal						calcium ion transport|response to pH|signal transduction	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(1)	1					Amiloride(DB00594)													---	---	---	---
DIP2B	57609	broad.mit.edu	37	12	50949841	50949841	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50949841delT	uc001rwv.2	+						DIP2B_uc001rwu.2_Intron	NM_173602	NP_775873			DIP2 disco-interacting protein 2 homolog B							nucleus	catalytic activity|transcription factor binding			ovary(4)|breast(1)|pancreas(1)	6																		---	---	---	---
DIP2B	57609	broad.mit.edu	37	12	50970149	50970149	+	Intron	DEL	A	-	-	rs35895556		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50970149delA	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																		---	---	---	---
ATF1	466	broad.mit.edu	37	12	51209176	51209177	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51209176_51209177delTT	uc001rww.3	+						ATF1_uc010smu.1_Intron	NM_005171	NP_005162			activating transcription factor 1						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway				EWSR1/ATF1(323)|FUS/ATF1(4)	soft_tissue(321)|ovary(2)|NS(2)|bone(2)|skin(2)	329								T	EWSR1|FUS	malignant melanoma of soft parts |angiomatoid fibrous histiocytoma 								---	---	---	---
NR4A1	3164	broad.mit.edu	37	12	52442607	52442608	+	5'Flank	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52442607_52442608delTT	uc001rzs.2	+						NR4A1_uc010sno.1_Intron|NR4A1_uc001rzr.2_Intron|NR4A1_uc009zmb.1_5'Flank|NR4A1_uc001rzt.2_5'Flank	NM_002135	NP_002126			nuclear receptor subfamily 4, group A, member 1						nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor		steroid hormone receptor activity|zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(357;0.0967)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	52499265	52499265	+	Intron	DEL	G	-	-	rs147185545	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52499265delG	uc009zme.1	+											Homo sapiens olfactory receptor, family 7, subfamily E, member 47 pseudogene, mRNA (cDNA clone IMAGE:5590288).																														---	---	---	---
PCBP2	5094	broad.mit.edu	37	12	53849431	53849431	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53849431delT	uc001sdl.3	+						PCBP2_uc001sdc.3_Intron|PCBP2_uc001sdb.3_Intron|PCBP2_uc001sde.3_Intron|PCBP2_uc001sdi.3_Intron|PCBP2_uc001sdd.3_Intron|PCBP2_uc001sdf.3_Intron|PCBP2_uc009zna.2_Intron|PCBP2_uc010soh.1_Intron|PCBP2_uc009zmz.1_Intron	NM_001128911	NP_001122383			poly(rC) binding protein 2 isoform d						innate immune response|negative regulation of defense response to virus|negative regulation of type I interferon production|nuclear mRNA splicing, via spliceosome|proteasomal ubiquitin-dependent protein catabolic process|response to virus	cytosol|nucleoplasm|ribonucleoprotein complex	DNA binding|RNA binding|ubiquitin protein ligase binding				0																		---	---	---	---
ATF7	11016	broad.mit.edu	37	12	53916900	53916901	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53916900_53916901insT	uc001sdy.2	-						ATF7_uc010sok.1_Intron|ATF7_uc001sdz.2_Intron|ATF7_uc010sol.1_Intron	NM_001130059	NP_001123531			activating transcription factor 7 isoform 1						interspecies interaction between organisms	cytoplasm|nuclear periphery|nucleoplasm	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)	2																		---	---	---	---
ATF7	11016	broad.mit.edu	37	12	53970486	53970489	+	Intron	DEL	AAAC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53970486_53970489delAAAC	uc001sdy.2	-						ATF7_uc010sok.1_Intron|ATF7_uc001sdz.2_Intron|ATF7_uc010sol.1_Intron|ATF7_uc001sea.3_Intron|ATF7_uc001seb.3_Intron	NM_001130059	NP_001123531			activating transcription factor 7 isoform 1						interspecies interaction between organisms	cytoplasm|nuclear periphery|nucleoplasm	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	54351377	54351377	+	IGR	DEL	G	-	-	rs35722078		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54351377delG								HOXC12 (1029 upstream) : HOTAIR (4721 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	54593803	54593804	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54593803_54593804delAA								SMUG1 (11046 upstream) : CBX5 (30928 downstream)																																			---	---	---	---
CBX5	23468	broad.mit.edu	37	12	54640584	54640585	+	Intron	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54640584_54640585delAG	uc001sfh.3	-						CBX5_uc001sfk.3_Intron|CBX5_uc001sfi.3_Intron|CBX5_uc001sfj.3_Intron	NM_001127322	NP_001120794			heterochromatin protein 1-alpha						blood coagulation|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|nuclear centromeric heterochromatin|nuclear envelope|nucleolus|transcriptional repressor complex	methylated histone residue binding|protein binding, bridging|repressing transcription factor binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	55311433	55311433	+	IGR	DEL	A	-	-	rs78271972		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55311433delA								MUCL1 (59261 upstream) : KIAA0748 (32432 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	55431000	55431000	+	IGR	DEL	T	-	-	rs68172869		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55431000delT								NEUROD4 (7200 upstream) : OR9K2 (92553 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	55481224	55481225	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55481224_55481225delTT								NEUROD4 (57424 upstream) : OR9K2 (42328 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	55509160	55509160	+	IGR	DEL	A	-	-	rs112685793		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55509160delA								NEUROD4 (85360 upstream) : OR9K2 (14393 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	55616089	55616090	+	IGR	INS	-	T	T	rs3947764	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55616089_55616090insT								OR10A7 (331 upstream) : OR6C74 (24982 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	55618292	55618294	+	IGR	DEL	GCG	-	-	rs144604313		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55618292_55618294delGCG								OR10A7 (2534 upstream) : OR6C74 (22778 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	55930442	55930442	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55930442delA								OR6C68 (43344 upstream) : OR6C4 (14569 downstream)																																			---	---	---	---
SMARCC2	6601	broad.mit.edu	37	12	56564203	56564203	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56564203delT	uc001skb.2	-						SMARCC2_uc001skd.2_Intron|SMARCC2_uc001ska.2_Intron|SMARCC2_uc001skc.2_Intron|SMARCC2_uc010sqf.1_Intron	NM_003075	NP_003066			SWI/SNF-related matrix-associated						chromatin remodeling|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			lung(2)|central_nervous_system(2)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(18;0.123)															---	---	---	---
PAN2	9924	broad.mit.edu	37	12	56716549	56716549	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56716549delG	uc001skx.2	-						PAN2_uc001skw.2_5'UTR|PAN2_uc001skz.2_Intron|PAN2_uc001sky.2_Intron	NM_001127460	NP_001120932			PAN2 polyA specific ribonuclease subunit homolog						nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|ubiquitin-dependent protein catabolic process	cytosol|nucleus	nucleic acid binding|poly(A)-specific ribonuclease activity|ubiquitin thiolesterase activity			ovary(2)|skin(2)|large_intestine(1)|breast(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	56896112	56896112	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56896112delT								GLS2 (13931 upstream) : RBMS2 (19497 downstream)																																			---	---	---	---
PTGES3	10728	broad.mit.edu	37	12	57065188	57065188	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57065188delA	uc001slu.3	-						PTGES3_uc001slw.3_Intron|PTGES3_uc010sqs.1_Intron|PTGES3_uc001slv.3_Intron|PTGES3_uc010sqt.1_Intron|PTGES3_uc009zox.2_Intron	NM_006601	NP_006592			prostaglandin-E synthase 3						chaperone cofactor-dependent protein refolding|hormone biosynthetic process|prostaglandin biosynthetic process|signal transduction|telomere maintenance	cytosol|telomerase holoenzyme complex	prostaglandin-E synthase activity|telomerase activity|unfolded protein binding				0																		---	---	---	---
TMEM194A	23306	broad.mit.edu	37	12	57466469	57466469	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57466469delT	uc001smy.2	-						TMEM194A_uc001smx.2_Intron|TMEM194A_uc010sra.1_Intron	NM_001130963	NP_001124435			transmembrane protein 194A isoform a							integral to membrane					0																		---	---	---	---
R3HDM2	22864	broad.mit.edu	37	12	57678656	57678656	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57678656delT	uc009zpm.1	-						R3HDM2_uc010srn.1_Intron|R3HDM2_uc001snu.2_5'Flank|R3HDM2_uc001snr.2_Intron|R3HDM2_uc001sns.2_Intron|R3HDM2_uc001snt.2_Intron	NM_014925	NP_055740			R3H domain containing 2							nucleus	nucleic acid binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	58275946	58275946	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58275946delT								CTDSP2 (35199 upstream) : XRCC6BP1 (59499 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	58298082	58298082	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58298082delT								CTDSP2 (57335 upstream) : XRCC6BP1 (37363 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	59557764	59557764	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:59557764delT								LRIG3 (243502 upstream) : SLC16A7 (432084 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	59796056	59796056	+	IGR	DEL	A	-	-	rs63279960		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:59796056delA								LRIG3 (481794 upstream) : SLC16A7 (193792 downstream)																																			---	---	---	---
SLC16A7	9194	broad.mit.edu	37	12	60064196	60064196	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:60064196delC	uc001sqs.2	+						SLC16A7_uc001sqt.2_Intron	NM_004731	NP_004722			solute carrier family 16, member 7							integral to plasma membrane|membrane fraction	pyruvate secondary active transmembrane transporter activity|secondary active monocarboxylate transmembrane transporter activity|symporter activity			ovary(1)	1				GBM - Glioblastoma multiforme(3;0.0303)	Pyruvic acid(DB00119)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	60183972	60183972	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:60183972delT								SLC16A7 (8565 upstream) : None (None downstream)																																			---	---	---	---
FAM19A2	338811	broad.mit.edu	37	12	62275701	62275701	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62275701delA	uc001sqw.2	-						FAM19A2_uc001sqx.2_Intron|FAM19A2_uc001sqy.2_Intron	NM_178539	NP_848634			family with sequence similarity 19 (chemokine							cytoplasm				ovary(1)	1			GBM - Glioblastoma multiforme(1;0.00484)	GBM - Glioblastoma multiforme(3;0.02)														---	---	---	---
FAM19A2	338811	broad.mit.edu	37	12	62408247	62408247	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62408247delA	uc001sqw.2	-						FAM19A2_uc001sqx.2_Intron|FAM19A2_uc001sqy.2_Intron	NM_178539	NP_848634			family with sequence similarity 19 (chemokine							cytoplasm				ovary(1)	1			GBM - Glioblastoma multiforme(1;0.00484)	GBM - Glioblastoma multiforme(3;0.02)														---	---	---	---
FAM19A2	338811	broad.mit.edu	37	12	62457637	62457638	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62457637_62457638delAC	uc001sqw.2	-						FAM19A2_uc001sqx.2_Intron|FAM19A2_uc001sqy.2_Intron	NM_178539	NP_848634			family with sequence similarity 19 (chemokine							cytoplasm				ovary(1)	1			GBM - Glioblastoma multiforme(1;0.00484)	GBM - Glioblastoma multiforme(3;0.02)														---	---	---	---
SRGAP1	57522	broad.mit.edu	37	12	64315762	64315763	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64315762_64315763delTT	uc010ssp.1	+						SRGAP1_uc001srt.2_Intron	NM_020762	NP_065813			SLIT-ROBO Rho GTPase activating protein 1						axon guidance	cytosol				ovary(2)|central_nervous_system(2)	4			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)														---	---	---	---
SRGAP1	57522	broad.mit.edu	37	12	64426159	64426159	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64426159delT	uc010ssp.1	+						SRGAP1_uc001srt.2_Intron|SRGAP1_uc001srv.2_Intron	NM_020762	NP_065813			SLIT-ROBO Rho GTPase activating protein 1						axon guidance	cytosol				ovary(2)|central_nervous_system(2)	4			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)														---	---	---	---
C12orf56	115749	broad.mit.edu	37	12	64661488	64661488	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64661488delA	uc001ssa.3	-						uc001srx.2_Intron|C12orf56_uc001sry.2_Intron|C12orf56_uc001srz.2_Intron	NM_001099676	NP_001093146			hypothetical protein LOC115749												0			GBM - Glioblastoma multiforme(3;0.000582)	GBM - Glioblastoma multiforme(28;0.0259)														---	---	---	---
C12orf56	115749	broad.mit.edu	37	12	64746630	64746631	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64746630_64746631delTT	uc001ssa.3	-						uc001srx.2_Intron	NM_001099676	NP_001093146			hypothetical protein LOC115749												0			GBM - Glioblastoma multiforme(3;0.000582)	GBM - Glioblastoma multiforme(28;0.0259)														---	---	---	---
GNS	2799	broad.mit.edu	37	12	65133419	65133419	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65133419delA	uc001ssg.3	-						GNS_uc001ssf.2_Intron|GNS_uc010ssq.1_Intron|GNS_uc010ssr.1_Intron	NM_002076	NP_002067			glucosamine (N-acetyl)-6-sulfatase precursor							lysosome	metal ion binding|N-acetylglucosamine-6-sulfatase activity|protein binding			central_nervous_system(1)	1	Lung NSC(1;7.25e-14)|all_lung(1;1.25e-12)		LUAD - Lung adenocarcinoma(6;0.115)	GBM - Glioblastoma multiforme(28;0.0435)														---	---	---	---
MSRB3	253827	broad.mit.edu	37	12	65726072	65726073	+	Intron	INS	-	GT	GT	rs143303839	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65726072_65726073insGT	uc001ssn.2	+						MSRB3_uc001ssm.2_Intron|MSRB3_uc009zqp.2_Intron	NM_198080	NP_932346			methionine sulfoxide reductase B3 isoform 1						protein repair	endoplasmic reticulum|mitochondrion	peptide-methionine-(S)-S-oxide reductase activity|protein-methionine-R-oxide reductase activity|zinc ion binding			central_nervous_system(1)|skin(1)	2			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.131)														---	---	---	---
MSRB3	253827	broad.mit.edu	37	12	65807563	65807563	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65807563delA	uc001ssn.2	+						MSRB3_uc001ssm.2_Intron|MSRB3_uc009zqp.2_Intron	NM_198080	NP_932346			methionine sulfoxide reductase B3 isoform 1						protein repair	endoplasmic reticulum|mitochondrion	peptide-methionine-(S)-S-oxide reductase activity|protein-methionine-R-oxide reductase activity|zinc ion binding			central_nervous_system(1)|skin(1)	2			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.131)														---	---	---	---
HMGA2	8091	broad.mit.edu	37	12	66298963	66298964	+	Intron	DEL	CA	-	-	rs71660511		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66298963_66298964delCA	uc001ssx.2	+						HMGA2_uc001ssw.1_Intron|HMGA2_uc001ssu.1_Intron|HMGA2_uc001ssv.2_Intron	NM_003483	NP_003474			high mobility group AT-hook 2 isoform a						cell division|chromatin organization|mitosis|multicellular organismal development|regulation of growth|transcription, DNA-dependent	chromatin	AT DNA binding		HMGA2/LPP(161)|HMGA2/WIF1_ENST00000286574(14)|HMGA2/RAD51B(11)|HMGA2/NFIB_ENST00000397581(8)|HMGA2/FHIT_ENST00000476844(4)|HMGA2/CCNB1IP1(2)|HMGA2/ALDH2_ENST00000261733(2)|HMGA2/EBF1(2)|HMGA2/LHFP(2)|HMGA2/COX6C(2)	soft_tissue(159)|bone(27)|salivary_gland(22)	208	all_cancers(1;5.78e-46)		GBM - Glioblastoma multiforme(1;0.00179)|LUSC - Lung squamous cell carcinoma(43;0.156)	GBM - Glioblastoma multiforme(28;0.0386)				T	 LHFP|RAD51L1|LPP|HEI10|COX6C|CMKOR1|NFIB|ALDH2|CCNB1IP1|EBF1|WIF1|FHIT	lipoma|leiomyoma|pleiomorphic salivary gland adenoma								---	---	---	---
TMBIM4	51643	broad.mit.edu	37	12	66531937	66531937	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66531937delA	uc001stc.2	-	7	596	c.520delT	c.(520-522)TATfs	p.Y174fs	LLPH_uc010ssx.1_Intron|TMBIM4_uc001std.2_Frame_Shift_Del_p.Y143fs|TMBIM4_uc009zqr.2_Frame_Shift_Del_p.Y221fs|TMBIM4_uc001ste.2_RNA|TMBIM4_uc001stf.2_Frame_Shift_Del_p.L162fs|TMBIM4_uc009zqs.2_Frame_Shift_Del_p.F158fs	NM_016056	NP_057140	Q9HC24	TMBI4_HUMAN	transmembrane BAX inhibitor motif containing 4	174						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	67151196	67151196	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67151196delT	uc010sta.1	-							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	67373124	67373125	+	IGR	DEL	AA	-	-	rs34424434		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67373124_67373125delAA								GRIP1 (175230 upstream) : CAND1 (289936 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	68171408	68171409	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68171408_68171409delTT								DYRK2 (114965 upstream) : IFNG (377141 downstream)																																			---	---	---	---
RAP1B	5908	broad.mit.edu	37	12	69020555	69020555	+	Intron	DEL	T	-	-	rs74812051		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69020555delT	uc001sub.2	+						RAP1B_uc010ste.1_Intron|RAP1B_uc001suc.2_Intron|RAP1B_uc010stf.1_Intron|RAP1B_uc010stg.1_Intron|RAP1B_uc010sth.1_Intron|RAP1B_uc010sti.1_Intron	NM_001089704	NP_001083173			SubName: Full=Ras-related protein Rap-1A; SubName: Full=cDNA FLJ75985, highly similar to Homo sapiens RAP1A, member of RAS oncogene family (RAP1A), transcript variant 2, mRNA; SubName: Full=RAP1A, member of RAS oncogene family;						blood coagulation|energy reserve metabolic process|regulation of establishment of cell polarity|regulation of insulin secretion	cell-cell junction|cytosol	GDP binding|GTP binding|GTPase activity|protein binding				0	Breast(13;1.24e-05)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)	GBM - Glioblastoma multiforme(7;0.000306)														---	---	---	---
NUP107	57122	broad.mit.edu	37	12	69126366	69126366	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69126366delA	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	69594093	69594102	+	IGR	DEL	AGAAAGAGAT	-	-	rs80081772		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69594093_69594102delAGAAAGAGAT								CPM (237073 upstream) : CPSF6 (39215 downstream)																																			---	---	---	---
FRS2	10818	broad.mit.edu	37	12	69861944	69861944	+	5'Flank	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69861944delA	uc001suy.2	+						FRS2_uc001suz.2_5'Flank|FRS2_uc009zrj.2_5'Flank|FRS2_uc009zrk.2_5'Flank	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	70378402	70378402	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70378402delA								RAB3IP (161420 upstream) : CNOT2 (258375 downstream)																																			---	---	---	---
PTPRR	5801	broad.mit.edu	37	12	71190487	71190487	+	Intron	DEL	A	-	-	rs146548068		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71190487delA	uc001swi.1	-							NM_002849	NP_002840			protein tyrosine phosphatase, receptor type, R						in utero embryonic development	cell surface|Golgi apparatus|integral to membrane|nucleus|perinuclear region of cytoplasm|plasma membrane	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			skin(2)|ovary(1)	3			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)														---	---	---	---
LGR5	8549	broad.mit.edu	37	12	71850778	71850778	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71850778delT	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																		---	---	---	---
TMEM19	55266	broad.mit.edu	37	12	72090433	72090434	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72090433_72090434insT	uc001sws.2	+						TMEM19_uc001swr.1_Intron|TMEM19_uc009zru.1_Intron	NM_018279	NP_060749			transmembrane protein 19							integral to membrane					0		Breast(359;0.0889)		GBM - Glioblastoma multiforme(134;0.044)														---	---	---	---
RAB21	23011	broad.mit.edu	37	12	72154498	72154498	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72154498delT	uc001swt.2	+							NM_014999	NP_055814			RAB21, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	cleavage furrow|cytoplasmic vesicle membrane|early endosome membrane|endoplasmic reticulum membrane|Golgi membrane	GDP binding|GTP binding|GTPase activity|protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	72428937	72428937	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72428937delT								TPH2 (2716 upstream) : LOC283392 (227391 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	73413317	73413317	+	IGR	DEL	G	-	-	rs112188296		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:73413317delG								TRHDE (353896 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	74109688	74109690	+	IGR	DEL	AGG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:74109688_74109690delAGG								None (None upstream) : ATXN7L3B (821861 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	74715824	74715824	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:74715824delT								None (None upstream) : ATXN7L3B (215727 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	74793526	74793527	+	IGR	DEL	TT	-	-	rs79433836		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:74793526_74793527delTT								None (None upstream) : ATXN7L3B (138024 downstream)																																			---	---	---	---
KCNC2	3747	broad.mit.edu	37	12	75538729	75538729	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75538729delA	uc001sxg.1	-						KCNC2_uc009zry.2_Intron|KCNC2_uc001sxe.2_Intron|KCNC2_uc001sxf.2_Intron|KCNC2_uc010stw.1_Intron	NM_139137	NP_631875			Shaw-related voltage-gated potassium channel						energy reserve metabolic process|regulation of insulin secretion	voltage-gated potassium channel complex	voltage-gated potassium channel activity			breast(2)|pancreas(2)|skin(1)|lung(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	75828750	75828750	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75828750delT								GLIPR1L2 (3159 upstream) : GLIPR1 (45763 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	76644723	76644724	+	IGR	DEL	TT	-	-	rs74701936		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76644723_76644724delTT								NAP1L1 (165985 upstream) : BBS10 (93542 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	76974126	76974126	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76974126delT								OSBPL8 (20537 upstream) : ZDHHC17 (183728 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	79211331	79211332	+	IGR	INS	-	T	T	rs4842302	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79211331_79211332insT								NAV3 (604543 upstream) : SYT1 (46441 downstream)																																			---	---	---	---
SYT1	6857	broad.mit.edu	37	12	79351526	79351527	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79351526_79351527insT	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																		---	---	---	---
PTPRQ	374462	broad.mit.edu	37	12	80970431	80970431	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80970431delT	uc001sze.2	+							NM_001145026	NP_001138498			protein tyrosine phosphatase, receptor type, Q												0																		---	---	---	---
PTPRQ	374462	broad.mit.edu	37	12	81035742	81035745	+	Intron	DEL	TTCT	-	-	rs71642352		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81035742_81035745delTTCT	uc001sze.2	+							NM_001145026	NP_001138498			protein tyrosine phosphatase, receptor type, Q												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	82435414	82435414	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82435414delT								PPFIA2 (282305 upstream) : CCDC59 (310676 downstream)																																			---	---	---	---
C12orf26	84190	broad.mit.edu	37	12	82871011	82871011	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82871011delT	uc001szq.2	+							NM_032230	NP_115606			hypothetical protein LOC84190												0																		---	---	---	---
TMTC2	160335	broad.mit.edu	37	12	83270837	83270837	+	Intron	DEL	T	-	-	rs11362075		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83270837delT	uc001szt.2	+						TMTC2_uc001szr.1_Intron|TMTC2_uc001szs.1_Intron|TMTC2_uc010suk.1_Intron	NM_152588	NP_689801			transmembrane and tetratricopeptide repeat							endoplasmic reticulum|integral to membrane	binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	83827598	83827598	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83827598delT								TMTC2 (299535 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	84412290	84412290	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:84412290delA								TMTC2 (884227 upstream) : SLC6A15 (840979 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	85312747	85312747	+	IGR	DEL	A	-	-	rs139009208		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85312747delA								SLC6A15 (6141 upstream) : TSPAN19 (95348 downstream)																																			---	---	---	---
LRRIQ1	84125	broad.mit.edu	37	12	85499220	85499220	+	Intron	DEL	T	-	-	rs138405454	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85499220delT	uc001tac.2	+						LRRIQ1_uc001tab.1_Intron	NM_001079910	NP_001073379			leucine-rich repeats and IQ motif containing 1											ovary(4)|central_nervous_system(1)|skin(1)	6				GBM - Glioblastoma multiforme(134;0.212)														---	---	---	---
LRRIQ1	84125	broad.mit.edu	37	12	85554294	85554294	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85554294delT	uc001tac.2	+							NM_001079910	NP_001073379			leucine-rich repeats and IQ motif containing 1											ovary(4)|central_nervous_system(1)|skin(1)	6				GBM - Glioblastoma multiforme(134;0.212)														---	---	---	---
ALX1	8092	broad.mit.edu	37	12	85674861	85674861	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85674861delT	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)														---	---	---	---
MGAT4C	25834	broad.mit.edu	37	12	87029435	87029436	+	Intron	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:87029435_87029436delTG	uc001tal.3	-						MGAT4C_uc001taj.3_Intron|MGAT4C_uc001tak.3_Intron	NM_013244	NP_037376			alpha-1,3-mannosyl-glycoprotein						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(3)	3																		---	---	---	---
MGAT4C	25834	broad.mit.edu	37	12	87125304	87125304	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:87125304delT	uc001tal.3	-						MGAT4C_uc001taj.3_Intron|MGAT4C_uc001tak.3_Intron	NM_013244	NP_037376			alpha-1,3-mannosyl-glycoprotein						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	87346815	87346818	+	IGR	DEL	GTGT	-	-	rs71930505		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:87346815_87346818delGTGT								MGAT4C (114134 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	87946749	87946749	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:87946749delT								MGAT4C (714068 upstream) : C12orf50 (427067 downstream)																																			---	---	---	---
CEP290	80184	broad.mit.edu	37	12	88454342	88454342	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88454342delA	uc001tar.2	-						CEP290_uc001taq.2_Intron	NM_025114	NP_079390			centrosomal protein 290kDa						cilium assembly|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|positive regulation of transcription, DNA-dependent|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding			ovary(5)|breast(1)|pancreas(1)	7																		---	---	---	---
CEP290	80184	broad.mit.edu	37	12	88482780	88482780	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88482780delA	uc001tar.2	-						CEP290_uc001taq.2_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	89051923	89051924	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89051923_89051924delTT								KITLG (77685 upstream) : DUSP6 (689915 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	89472077	89472077	+	IGR	DEL	A	-	-	rs62703160		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89472077delA								KITLG (497839 upstream) : DUSP6 (269762 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	89703190	89703190	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89703190delA								KITLG (728952 upstream) : DUSP6 (38649 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	90150510	90150510	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90150510delT								LOC338758 (44782 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	90484023	90484023	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90484023delT								LOC338758 (378295 upstream) : C12orf12 (861970 downstream)																																			---	---	---	---
EPYC	1833	broad.mit.edu	37	12	91366471	91366472	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91366471_91366472insA	uc001tbk.2	-							NM_004950	NP_004941			dermatan sulfate proteoglycan 3 precursor						female pregnancy	proteinaceous extracellular matrix	glycosaminoglycan binding			skin(1)	1																		---	---	---	---
BTG1	694	broad.mit.edu	37	12	92446621	92446621	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92446621delA	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	92932568	92932568	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92932568delA								CLLU1 (55112 upstream) : C12orf74 (164272 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	93114100	93114101	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93114100_93114101delTT								C12orf74 (11776 upstream) : PLEKHG7 (16164 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	93998741	93998743	+	IGR	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93998741_93998743delTTT								SOCS2 (28763 upstream) : CRADD (72408 downstream)																																			---	---	---	---
PLXNC1	10154	broad.mit.edu	37	12	94675906	94675910	+	Intron	DEL	AAAGT	-	-	rs2307570		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94675906_94675910delAAAGT	uc001tdc.2	+						PLXNC1_uc010sut.1_Intron|PLXNC1_uc009zsv.2_Intron	NM_005761	NP_005752			plexin C1 precursor						axon guidance|cell adhesion	integral to membrane|intracellular|plasma membrane	receptor activity|receptor binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	95410155	95410155	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95410155delT								NDUFA12 (12644 upstream) : NR2C1 (3905 downstream)																																			---	---	---	---
FGD6	55785	broad.mit.edu	37	12	95582159	95582160	+	Intron	DEL	GT	-	-	rs72331830		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95582159_95582160delGT	uc001tdp.3	-						FGD6_uc009zsx.2_Intron	NM_018351	NP_060821			FYVE, RhoGEF and PH domain containing 6						actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(2)|breast(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	96009974	96009974	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96009974delG								USP44 (64711 upstream) : NTN4 (41610 downstream)																																			---	---	---	---
CCDC38	120935	broad.mit.edu	37	12	96284755	96284755	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96284755delA	uc001tek.1	-							NM_182496	NP_872302			coiled-coil domain containing 38											skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	96845482	96845487	+	IGR	DEL	ACACAC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96845482_96845487delACACAC								CDK17 (51259 upstream) : C12orf63 (196266 downstream)																																			---	---	---	---
C12orf63	374467	broad.mit.edu	37	12	97082938	97082938	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97082938delT	uc001tet.1	+							NM_198520	NP_940922			hypothetical protein LOC374467											skin(6)|ovary(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	97981647	97981647	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97981647delA								RMST (22854 upstream) : LOC100128191 (925106 downstream)																																			---	---	---	---
ANKS1B	56899	broad.mit.edu	37	12	99885085	99885086	+	Intron	DEL	AA	-	-	rs34977034		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99885085_99885086delAA	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc009ztt.1_Intron	NM_152788	NP_690001			cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)														---	---	---	---
ANKS1B	56899	broad.mit.edu	37	12	100040768	100040768	+	Intron	DEL	A	-	-	rs71742846		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100040768delA	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc009ztt.1_Intron|FAM71C_uc001tgn.2_5'Flank	NM_152788	NP_690001			cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)														---	---	---	---
UHRF1BP1L	23074	broad.mit.edu	37	12	100530291	100530292	+	Intron	DEL	AT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100530291_100530292delAT	uc001tgq.2	-						UHRF1BP1L_uc001tgr.2_Intron	NM_015054	NP_055869			UHRF1 (ICBP90) binding protein 1-like isoform a											ovary(2)	2																		---	---	---	---
UHRF1BP1L	23074	broad.mit.edu	37	12	100532645	100532646	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100532645_100532646delAC	uc001tgq.2	-						UHRF1BP1L_uc001tgr.2_Intron	NM_015054	NP_055869			UHRF1 (ICBP90) binding protein 1-like isoform a											ovary(2)	2																		---	---	---	---
UHRF1BP1L	23074	broad.mit.edu	37	12	100536987	100536987	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100536987delT	uc001tgq.2	-						UHRF1BP1L_uc001tgr.2_5'Flank	NM_015054	NP_055869			UHRF1 (ICBP90) binding protein 1-like isoform a											ovary(2)	2																		---	---	---	---
DEPDC4	120863	broad.mit.edu	37	12	100657163	100657163	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100657163delT	uc001thi.2	-						DEPDC4_uc001thh.1_Intron|DEPDC4_uc001thj.1_Intron|DEPDC4_uc009ztv.1_Intron|DEPDC4_uc001thk.1_Intron|DEPDC4_uc001thl.1_Intron	NM_152317	NP_689530			DEP domain containing 4						intracellular signal transduction						0																		---	---	---	---
SCYL2	55681	broad.mit.edu	37	12	100709304	100709304	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100709304delT	uc001thn.2	+						SCYL2_uc009ztw.1_Intron|SCYL2_uc001thm.1_Intron	NM_017988	NP_060458			SCY1-like 2 protein						endosome to lysosome transport|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of clathrin-mediated endocytosis|positive regulation of receptor internalization	clathrin-coated vesicle|endosome membrane|Golgi apparatus|perinuclear region of cytoplasm	ATP binding|protein kinase activity|receptor binding			lung(3)|ovary(2)|skin(1)	6																		---	---	---	---
ANO4	121601	broad.mit.edu	37	12	101238552	101238555	+	Intron	DEL	AGTC	-	-	rs140485726		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101238552_101238555delAGTC	uc010svm.1	+						ANO4_uc010svl.1_Intron|ANO4_uc001thw.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	101679507	101679507	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101679507delT	uc001tia.1	+						UTP20_uc009ztz.1_Intron	NM_014503	NP_055318			down-regulated in metastasis						endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation	90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome	protein binding			ovary(2)|breast(2)	4																		---	---	---	---
UTP20	27340	broad.mit.edu	37	12	101700374	101700374	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101700374delT	uc001tia.1	+							NM_014503	NP_055318			down-regulated in metastasis						endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation	90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome	protein binding			ovary(2)|breast(2)	4																		---	---	---	---
UTP20	27340	broad.mit.edu	37	12	101738703	101738703	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101738703delT	uc001tia.1	+							NM_014503	NP_055318			down-regulated in metastasis						endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation	90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome	protein binding			ovary(2)|breast(2)	4																		---	---	---	---
UTP20	27340	broad.mit.edu	37	12	101769713	101769713	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101769713delA	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	102676752	102676752	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102676752delT								PMCH (85138 upstream) : IGF1 (112893 downstream)																																			---	---	---	---
IGF1	3479	broad.mit.edu	37	12	102836226	102836226	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102836226delT	uc001tjp.3	-						IGF1_uc001tjn.2_Intron|IGF1_uc001tjm.2_Intron|IGF1_uc001tjo.2_Intron	NM_001111285	NP_001104755			insulin-like growth factor 1 isoform 3						anti-apoptosis|bone mineralization involved in bone maturation|cellular component movement|DNA replication|glycolate metabolic process|muscle hypertrophy|myoblast differentiation|myoblast proliferation|myotube cell development|negative regulation of smooth muscle cell apoptosis|phosphatidylinositol-mediated signaling|platelet activation|platelet degranulation|positive regulation of activated T cell proliferation|positive regulation of DNA replication|positive regulation of epithelial cell proliferation|positive regulation of fibroblast proliferation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis|positive regulation of osteoblast differentiation|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of Ras protein signal transduction|positive regulation of smooth muscle cell migration|positive regulation of smooth muscle cell proliferation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tyrosine phosphorylation of Stat5 protein|Ras protein signal transduction|regulation of multicellular organism growth|satellite cell maintenance involved in skeletal muscle regeneration	platelet alpha granule lumen	growth factor activity|hormone activity|insulin receptor binding|insulin-like growth factor receptor binding|integrin binding			central_nervous_system(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	103628240	103628241	+	IGR	INS	-	A	A	rs144395921	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103628240_103628241insA								ASCL1 (273953 upstream) : C12orf42 (3129 downstream)																																			---	---	---	---
C12orf42	374470	broad.mit.edu	37	12	103793288	103793292	+	Intron	DEL	AAAAG	-	-	rs146664936		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103793288_103793292delAAAAG	uc001tjt.2	-						C12orf42_uc001tjs.2_Intron|C12orf42_uc009zuf.1_Intron|C12orf42_uc001tju.2_Intron	NM_198521	NP_940923			hypothetical protein LOC374470											ovary(1)|central_nervous_system(1)	2																		---	---	---	---
STAB2	55576	broad.mit.edu	37	12	104086174	104086175	+	Intron	INS	-	G	G	rs141655395	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104086174_104086175insG	uc001tjw.2	+							NM_017564	NP_060034			stabilin 2 precursor						angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14																		---	---	---	---
STAB2	55576	broad.mit.edu	37	12	104127181	104127181	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104127181delT	uc001tjw.2	+						STAB2_uc009zug.2_Intron	NM_017564	NP_060034			stabilin 2 precursor						angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14																		---	---	---	---
GLT8D2	83468	broad.mit.edu	37	12	104396862	104396863	+	Intron	DEL	GA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104396862_104396863delGA	uc001tkh.1	-						GLT8D2_uc001tki.1_Intron	NM_031302	NP_112592			glycosyltransferase 8 domain containing 2							integral to membrane	transferase activity, transferring glycosyl groups			ovary(1)|skin(1)	2																		---	---	---	---
CHST11	50515	broad.mit.edu	37	12	104893464	104893464	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104893464delA	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	105114510	105114510	+	Intron	DEL	A	-	-	rs10711712		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105114510delA	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	105162399	105162402	+	IGR	DEL	TTTA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105162399_105162402delTTTA								CHST11 (10516 upstream) : SLC41A2 (34874 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	105360281	105360281	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105360281delA								SLC41A2 (37809 upstream) : C12orf45 (19817 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	105368472	105368472	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105368472delA								SLC41A2 (46000 upstream) : C12orf45 (11626 downstream)																																			---	---	---	---
ALDH1L2	160428	broad.mit.edu	37	12	105456116	105456117	+	Intron	INS	-	GGACTCTTAA	GGACTCTTAA	rs142424730	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105456116_105456117insGGACTCTTAA	uc001tlc.2	-						ALDH1L2_uc009zuo.2_Intron|ALDH1L2_uc009zup.2_Intron	NM_001034173	NP_001029345			aldehyde dehydrogenase 1 family, member L2						10-formyltetrahydrofolate catabolic process|biosynthetic process	mitochondrion	acyl carrier activity|cofactor binding|formyltetrahydrofolate dehydrogenase activity|hydroxymethyl-, formyl- and related transferase activity|methyltransferase activity|phosphopantetheine binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	107161766	107161766	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107161766delA								RFX4 (5186 upstream) : RIC8B (6633 downstream)																																			---	---	---	---
PRDM4	11108	broad.mit.edu	37	12	108137896	108137897	+	Intron	DEL	AG	-	-	rs1344539	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108137896_108137897delAG	uc001tmp.2	-						PRDM4_uc010sww.1_5'Flank|PRDM4_uc001tmq.2_Intron	NM_012406	NP_036538			PR domain containing 4						cell proliferation|negative regulation of cell cycle|nerve growth factor receptor signaling pathway|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding			breast(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	108354457	108354457	+	IGR	DEL	T	-	-	rs75706448		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108354457delT								ASCL4 (184037 upstream) : WSCD2 (169054 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	108772630	108772630	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108772630delA								CMKLR1 (39536 upstream) : FICD (136421 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	108905394	108905394	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108905394delA								CMKLR1 (172300 upstream) : FICD (3657 downstream)																																			---	---	---	---
SART3	9733	broad.mit.edu	37	12	108946850	108946850	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108946850delA	uc001tmz.1	-						SART3_uc009zux.1_Intron|SART3_uc010swx.1_Intron|SART3_uc010swz.1_Intron|SART3_uc001tna.1_Intron	NM_014706	NP_055521			squamous cell carcinoma antigen recognized by T						RNA processing	cytoplasm|nuclear speck	nucleotide binding|protein binding|RNA binding			pancreas(1)	1														Porokeratosis				---	---	---	---
MYO1H	283446	broad.mit.edu	37	12	109836386	109836386	+	Intron	DEL	A	-	-	rs35624373		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109836386delA	uc010sxn.1	+							NM_001101421	NP_001094891			myosin 1H							myosin complex	motor activity				0																		---	---	---	---
MYO1H	283446	broad.mit.edu	37	12	109838772	109838772	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109838772delA	uc010sxn.1	+							NM_001101421	NP_001094891			myosin 1H							myosin complex	motor activity				0																		---	---	---	---
C12orf76	400073	broad.mit.edu	37	12	110480873	110480873	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110480873delA	uc001tqd.1	-						C12orf76_uc001tqe.1_Intron|C12orf76_uc010sxx.1_Intron|C12orf76_uc001tqb.1_Intron|C12orf76_uc001tqc.1_Intron	NM_207435	NP_997318			hypothetical protein LOC400073											large_intestine(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	110558794	110558794	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110558794delA								C12orf76 (47355 upstream) : IFT81 (3346 downstream)																																			---	---	---	---
IFT81	28981	broad.mit.edu	37	12	110584610	110584610	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110584610delA	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	110648536	110648536	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110648536delA	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																		---	---	---	---
ARPC3	10094	broad.mit.edu	37	12	110875180	110875180	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110875180delT	uc001tqq.2	-							NM_005719	NP_005710			actin related protein 2/3 complex subunit 3						cellular component movement|regulation of actin filament polymerization	Arp2/3 protein complex|cytoplasm	actin binding|structural constituent of cytoskeleton			ovary(1)	1																		---	---	---	---
CCDC63	160762	broad.mit.edu	37	12	111281881	111281881	+	5'Flank	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111281881delA	uc001trv.1	+						CCDC63_uc009zvt.1_5'Flank|CCDC63_uc010sye.1_5'Flank|CCDC63_uc001trw.1_5'Flank	NM_152591	NP_689804			coiled-coil domain containing 63											skin(6)|ovary(1)|pancreas(1)	8																		---	---	---	---
CCDC63	160762	broad.mit.edu	37	12	111318583	111318584	+	Intron	INS	-	TGG	TGG			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111318583_111318584insTGG	uc001trv.1	+						CCDC63_uc009zvt.1_Intron|CCDC63_uc010sye.1_Intron|CCDC63_uc001trw.1_Intron	NM_152591	NP_689804			coiled-coil domain containing 63											skin(6)|ovary(1)|pancreas(1)	8																		---	---	---	---
CUX2	23316	broad.mit.edu	37	12	111785948	111785948	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111785948delC	uc001tsa.1	+	22	4433	c.4280delC	c.(4279-4281)GCCfs	p.A1427fs		NM_015267	NP_056082	O14529	CUX2_HUMAN	cut-like 2	1427	Pro-rich.					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	111971813	111971813	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111971813delA	uc001tsj.2	-						ATXN2_uc001tsh.2_Intron|ATXN2_uc001tsi.2_Intron|ATXN2_uc001tsk.2_Intron|ATXN2_uc001tsm.1_Intron	NM_002973	NP_002964			ataxin 2						cell death|cytoplasmic mRNA processing body assembly|regulation of translation|RNA metabolic process|RNA transport|stress granule assembly	nucleus|perinuclear region of cytoplasm|polysome|stress granule|trans-Golgi network	protein C-terminus binding|RNA binding			ovary(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	112052789	112052789	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112052789delT								ATXN2 (15309 upstream) : BRAP (27162 downstream)																																			---	---	---	---
ACAD10	80724	broad.mit.edu	37	12	112135050	112135050	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112135050delA	uc001tsq.2	+						ACAD10_uc009zvw.2_Intron|ACAD10_uc001tso.3_Intron|ACAD10_uc001tsp.2_Intron|ACAD10_uc009zvx.2_Intron	NM_025247	NP_079523			acyl-Coenzyme A dehydrogenase family, member 10								acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|hydrolase activity|transferase activity, transferring phosphorus-containing groups			ovary(2)	2																		---	---	---	---
MAPKAPK5	8550	broad.mit.edu	37	12	112303037	112303037	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112303037delT	uc001tta.2	+						MAPKAPK5_uc001tsz.2_Intron|MAPKAPK5_uc001ttb.2_5'Flank	NM_139078	NP_620777			MAP kinase-activated protein kinase 5 isoform 2						signal transduction	cytoplasm|nucleus	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity			lung(2)|ovary(1)	3																		---	---	---	---
TMEM116	89894	broad.mit.edu	37	12	112407589	112407589	+	Intron	DEL	G	-	-	rs111510050		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112407589delG	uc001ttc.1	-						TMEM116_uc001ttd.1_Intron|TMEM116_uc001tte.1_Intron|TMEM116_uc001ttf.1_Intron|TMEM116_uc001ttg.1_Intron|TMEM116_uc001tth.1_Intron|TMEM116_uc001tti.1_Intron	NM_138341	NP_612350			transmembrane protein 116							integral to membrane				ovary(1)	1																		---	---	---	---
NAA25	80018	broad.mit.edu	37	12	112499293	112499293	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112499293delA	uc001ttm.2	-						NAA25_uc001ttn.3_Intron|NAA25_uc009zvz.1_Intron|NAA25_uc009zwa.1_Intron	NM_024953	NP_079229			mitochondrial distribution and morphology 20							cytoplasm	protein binding			ovary(1)|breast(1)|pancreas(1)	3																		---	---	---	---
PTPN11	5781	broad.mit.edu	37	12	112943981	112943982	+	3'UTR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112943981_112943982insT	uc001ttx.2	+	16						NM_002834	NP_002825			protein tyrosine phosphatase, non-receptor type						axon guidance|cell junction assembly|ephrin receptor signaling pathway|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|platelet activation|regulation of cell adhesion mediated by integrin|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway	cytosol	non-membrane spanning protein tyrosine phosphatase activity|protein binding			haematopoietic_and_lymphoid_tissue(375)|lung(6)|autonomic_ganglia(2)|soft_tissue(2)|central_nervous_system(2)|large_intestine(1)|skin(1)|ovary(1)|NS(1)|kidney(1)	392								Mis		JMML|AML|MDS		Noonan Syndrome		Noonan_syndrome				---	---	---	---
RPH3A	22895	broad.mit.edu	37	12	113031984	113031984	+	Intron	DEL	C	-	-	rs34313792		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113031984delC	uc010syl.1	+							NM_001143854	NP_001137326			rabphilin 3A homolog isoform 1						intracellular protein transport	cell junction|synaptic vesicle	Rab GTPase binding|transporter activity|zinc ion binding			ovary(3)|central_nervous_system(2)|skin(2)	7				BRCA - Breast invasive adenocarcinoma(302;0.00453)														---	---	---	---
OAS2	4939	broad.mit.edu	37	12	113448898	113448898	+	3'UTR	DEL	T	-	-	rs34160651		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113448898delT	uc001tuj.2	+	11						NM_016817	NP_058197			2'-5'-oligoadenylate synthetase 2 isoform 1						interferon-gamma-mediated signaling pathway|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|type I interferon-mediated signaling pathway	endoplasmic reticulum|membrane|microsome|mitochondrion|nucleus	ATP binding|nucleotidyltransferase activity|RNA binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	113472557	113472557	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113472557delA								OAS2 (23030 upstream) : DTX1 (23105 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	113961104	113961104	+	IGR	DEL	T	-	-	rs78981086		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113961104delT								LHX5 (51227 upstream) : RBM19 (293439 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	114211756	114211756	+	5'Flank	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114211756delA	uc001tvk.1	-						uc001tvl.3_5'Flank					Homo sapiens cDNA FLJ39613 fis, clone SKNSH2009357.																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	114565672	114565674	+	IGR	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114565672_114565674delTTT								RBM19 (161496 upstream) : TBX5 (226062 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	114669155	114669155	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114669155delT								RBM19 (264979 upstream) : TBX5 (122581 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	114960127	114960128	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114960127_114960128delTT								TBX5 (113880 upstream) : TBX3 (147931 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	115078118	115078119	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115078118_115078119delTC								TBX5 (231871 upstream) : TBX3 (29940 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	115252074	115252074	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115252074delT								TBX3 (130105 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	115611439	115611439	+	IGR	DEL	A	-	-	rs35943369		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115611439delA								TBX3 (489470 upstream) : MED13L (784944 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	115860793	115860793	+	IGR	DEL	G	-	-	rs113520862		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115860793delG								TBX3 (738824 upstream) : MED13L (535590 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	116034833	116034833	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116034833delA								TBX3 (912864 upstream) : MED13L (361550 downstream)																																			---	---	---	---
MED13L	23389	broad.mit.edu	37	12	116470530	116470530	+	Intron	DEL	T	-	-	rs75656482		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116470530delT	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	116633463	116633463	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116633463delC	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-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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	116853607	116853608	+	IGR	DEL	GT	-	-	rs115658176	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116853607_116853608delGT								MED13L (138616 upstream) : NCRNA00173 (117619 downstream)																																			---	---	---	---
C12orf49	79794	broad.mit.edu	37	12	117164484	117164484	+	Intron	DEL	C	-	-	rs10711858		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117164484delC	uc001tvz.1	-						C12orf49_uc009zwm.1_Intron	NM_024738	NP_079014			hypothetical protein LOC79794 precursor							extracellular region				ovary(1)	1	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0281)														---	---	---	---
NOS1	4842	broad.mit.edu	37	12	117713247	117713247	+	Intron	DEL	C	-	-	rs7138586	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117713247delC	uc001twm.1	-							NM_000620	NP_000611			nitric oxide synthase 1, neuronal						multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia	cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum	arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding			ovary(3)|skin(3)|pancreas(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)	L-Citrulline(DB00155)													---	---	---	---
NOS1	4842	broad.mit.edu	37	12	117750663	117750665	+	Intron	DEL	ATC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117750663_117750665delATC	uc001twm.1	-							NM_000620	NP_000611			nitric oxide synthase 1, neuronal						multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia	cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum	arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding			ovary(3)|skin(3)|pancreas(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)	L-Citrulline(DB00155)													---	---	---	---
NOS1	4842	broad.mit.edu	37	12	117779917	117779917	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117779917delT	uc001twm.1	-							NM_000620	NP_000611			nitric oxide synthase 1, neuronal						multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia	cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum	arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding			ovary(3)|skin(3)|pancreas(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)	L-Citrulline(DB00155)													---	---	---	---
KSR2	283455	broad.mit.edu	37	12	118365507	118365507	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118365507delA	uc001two.2	-							NM_173598	NP_775869			kinase suppressor of ras 2						intracellular signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(10)|central_nervous_system(2)|stomach(1)|large_intestine(1)|breast(1)	15	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
KSR2	283455	broad.mit.edu	37	12	118395216	118395216	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118395216delT	uc001two.2	-							NM_173598	NP_775869			kinase suppressor of ras 2						intracellular signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(10)|central_nervous_system(2)|stomach(1)|large_intestine(1)|breast(1)	15	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	118914916	118914916	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118914916delC								SUDS3 (59077 upstream) : SRRM4 (504480 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	118966928	118966928	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118966928delT								SUDS3 (111089 upstream) : SRRM4 (452468 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	119232406	119232406	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119232406delT								SUDS3 (376567 upstream) : SRRM4 (186990 downstream)																																			---	---	---	---
SRRM4	84530	broad.mit.edu	37	12	119426934	119426934	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119426934delG	uc001txa.1	+							NM_194286	NP_919262			KIAA1853 protein						cell differentiation|mRNA processing|nervous system development|regulation of RNA splicing|RNA splicing	nucleus	mRNA binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	119764159	119764160	+	IGR	DEL	AC	-	-	rs66651215		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119764159_119764160delAC								LOC144742 (22974 upstream) : CCDC60 (8357 downstream)																																			---	---	---	---
CIT	11113	broad.mit.edu	37	12	120150675	120150675	+	Intron	DEL	A	-	-	rs113783917		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120150675delA	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	120194922	120194922	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120194922delA	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	120297618	120297618	+	Intron	DEL	A	-	-	rs79951590		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120297618delA	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)														---	---	---	---
GCN1L1	10985	broad.mit.edu	37	12	120577434	120577435	+	Intron	INS	-	A	A	rs112940934		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120577434_120577435insA	uc001txo.2	-							NM_006836	NP_006827			GCN1 general control of amino-acid synthesis						regulation of translation	ribosome	protein binding|translation factor activity, nucleic acid binding			ovary(4)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
PXN	5829	broad.mit.edu	37	12	120649920	120649920	+	3'UTR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120649920delG	uc001txt.2	-	12					uc001txs.1_Intron|PXN_uc001txu.2_3'UTR|PXN_uc001txv.2_3'UTR|PXN_uc001txx.2_3'UTR|PXN_uc001txy.2_3'UTR|PXN_uc001txz.2_RNA	NM_001080855	NP_001074324			paxillin isoform 1						cell junction assembly|cell-matrix adhesion|cellular response to reactive oxygen species|epidermal growth factor receptor signaling pathway|growth hormone receptor signaling pathway|muscle contraction|signal complex assembly	cytoplasm|focal adhesion|lamellipodium|microtubule associated complex	beta-catenin binding|vinculin binding|zinc ion binding			ovary(1)|breast(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
DYNLL1	8655	broad.mit.edu	37	12	120920486	120920486	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120920486delA	uc001tyj.2	+							NM_001037494	NP_001032583			dynein light chain 1						actin cytoskeleton organization|activation of pro-apoptotic gene products|anatomical structure morphogenesis|female gamete generation|G2/M transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|microtubule-based process|negative regulation of phosphorylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transport	centrosome|cytoplasmic dynein complex|cytosol|microtubule|mitochondrion|nucleus|plasma membrane	motor activity|protein binding				0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
COQ5	84274	broad.mit.edu	37	12	120968022	120968022	+	5'Flank	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120968022delA	uc001tyn.2	-						COQ5_uc001tyo.2_5'Flank|COQ5_uc010szj.1_5'Flank	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)																	---	---	---	---
SPPL3	121665	broad.mit.edu	37	12	121277654	121277654	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121277654delA	uc001tzd.2	-						SPPL3_uc009zwz.2_Intron	NM_139015	NP_620584			signal peptide peptidase 3							integral to membrane	aspartic-type endopeptidase activity				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	121563688	121563689	+	IGR	DEL	AA	-	-	rs34662655		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121563688_121563689delAA								OASL (86908 upstream) : P2RX7 (6989 downstream)																																			---	---	---	---
KDM2B	84678	broad.mit.edu	37	12	122018158	122018158	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122018158delG	uc001uat.2	-						KDM2B_uc001uas.2_5'UTR|KDM2B_uc001uau.2_Intron|KDM2B_uc001uav.3_Intron	NM_032590	NP_115979			F-box and leucine-rich repeat protein 10 isoform						embryonic camera-type eye morphogenesis|fourth ventricle development|histone H2A monoubiquitination|initiation of neural tube closure|lateral ventricle development|midbrain development|midbrain-hindbrain boundary morphogenesis|negative regulation of neural precursor cell proliferation|negative regulation of neuron apoptosis|negative regulation of transcription from RNA polymerase II promoter|spermatogenesis|third ventricle development|transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|rRNA binding|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	122032783	122032784	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122032783_122032784delAA								KDM2B (13863 upstream) : ORAI1 (31671 downstream)																																			---	---	---	---
MORN3	283385	broad.mit.edu	37	12	122094170	122094170	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122094170delT	uc001uax.2	-						MORN3_uc001uay.2_Intron	NM_173855	NP_776254			MORN repeat containing 3												0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000409)|Epithelial(86;0.00145)														---	---	---	---
VPS33A	65082	broad.mit.edu	37	12	122732607	122732608	+	Intron	INS	-	TG	TG	rs147581492	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122732607_122732608insTG	uc001ucd.2	-						VPS33A_uc001ucc.2_Intron	NM_022916	NP_075067			vacuolar protein sorting 33A						lysosome localization|melanosome localization|platelet formation|protein transport|regulation of developmental pigmentation|vesicle docking involved in exocytosis	early endosome|late endosome membrane|lysosomal membrane|perinuclear region of cytoplasm	protein binding			skin(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000336)|Epithelial(86;0.000606)|BRCA - Breast invasive adenocarcinoma(302;0.23)														---	---	---	---
CLIP1	6249	broad.mit.edu	37	12	122798282	122798282	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122798282delA	uc001ucg.1	-						CLIP1_uc001uch.1_Intron|CLIP1_uc001uci.1_Intron|CLIP1_uc001ucj.1_Intron	NM_002956	NP_002947			restin isoform a						mitotic prometaphase|positive regulation of microtubule polymerization	centrosome|cytosol|endosome|intermediate filament|kinetochore	nucleic acid binding|protein homodimerization activity|zinc ion binding			ovary(2)|breast(1)	3	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)														---	---	---	---
CLIP1	6249	broad.mit.edu	37	12	122800541	122800541	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122800541delT	uc001ucg.1	-						CLIP1_uc001uch.1_Intron|CLIP1_uc001uci.1_Intron|CLIP1_uc001ucj.1_Intron	NM_002956	NP_002947			restin isoform a						mitotic prometaphase|positive regulation of microtubule polymerization	centrosome|cytosol|endosome|intermediate filament|kinetochore	nucleic acid binding|protein homodimerization activity|zinc ion binding			ovary(2)|breast(1)	3	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	122949795	122949796	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122949795_122949796delAC								CLIP1 (42679 upstream) : ZCCHC8 (7640 downstream)																																			---	---	---	---
ZCCHC8	55596	broad.mit.edu	37	12	122962860	122962860	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122962860delA	uc001ucn.2	-						ZCCHC8_uc001ucl.2_5'UTR|ZCCHC8_uc001ucm.2_Intron|ZCCHC8_uc009zxp.2_Intron|ZCCHC8_uc009zxq.2_Intron	NM_017612	NP_060082			zinc finger, CCHC domain containing 8							catalytic step 2 spliceosome	nucleic acid binding|protein binding|zinc ion binding				0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.25e-05)|Epithelial(86;0.000113)|BRCA - Breast invasive adenocarcinoma(302;0.202)														---	---	---	---
RSRC2	65117	broad.mit.edu	37	12	122993996	122993997	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122993996_122993997insA	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)														---	---	---	---
DNAH10	196385	broad.mit.edu	37	12	124270504	124270504	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124270504delT	uc001uft.3	+							NM_207437	NP_997320			dynein, axonemal, heavy chain 10						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)														---	---	---	---
NCOR2	9612	broad.mit.edu	37	12	124975173	124975173	+	Intron	DEL	C	-	-	rs72334098		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124975173delC	uc010tba.1	-						NCOR2_uc010tay.1_Intron|NCOR2_uc010taz.1_Intron|NCOR2_uc010tbb.1_Intron|NCOR2_uc010tbc.1_Intron|NCOR2_uc001ugj.1_Intron|NCOR2_uc001ugk.1_Intron	NM_001077261	NP_001070729			nuclear receptor co-repressor 2 isoform 2						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	125531113	125531113	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125531113delA								BRI3BP (20764 upstream) : AACS (18812 downstream)																																			---	---	---	---
TMEM132B	114795	broad.mit.edu	37	12	125967997	125967997	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125967997delA	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	126077084	126077084	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126077084delA	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	126279724	126279726	+	IGR	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126279724_126279726delTTT								TMEM132B (136135 upstream) : LOC100128554 (647301 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	126478284	126478284	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126478284delT								TMEM132B (334695 upstream) : LOC100128554 (448743 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	126693103	126693103	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126693103delA								TMEM132B (549514 upstream) : LOC100128554 (233924 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	126918250	126918251	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126918250_126918251delAC								TMEM132B (774661 upstream) : LOC100128554 (8776 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	127151344	127151344	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127151344delT								LOC100128554 (194014 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	127448982	127448982	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127448982delA	uc001uho.2	-											Homo sapiens cDNA clone IMAGE:4829480.																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	127562509	127562510	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127562509_127562510delTC								LOC100128554 (605179 upstream) : None (None downstream)																																			---	---	---	---
TMEM132D	121256	broad.mit.edu	37	12	129824856	129824857	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129824856_129824857insT	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)														---	---	---	---
RIMBP2	23504	broad.mit.edu	37	12	131031767	131031767	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131031767delA	uc001uim.2	-											RecName: Full=RIMS-binding protein 2;          Short=RIM-BP2;							cell junction|synapse				upper_aerodigestive_tract(3)|ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	11	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	132183651	132183653	+	IGR	DEL	ATA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132183651_132183653delATA								LOC116437 (486176 upstream) : SFRS8 (11982 downstream)																																			---	---	---	---
SFRS8	6433	broad.mit.edu	37	12	132192711	132192711	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132192711delT	uc001uja.1	+						SFRS8_uc010tbn.1_5'Flank|SFRS8_uc001ujb.1_5'Flank|SFRS8_uc001uiz.1_5'Flank	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)														---	---	---	---
EP400	57634	broad.mit.edu	37	12	132548051	132548051	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132548051delA	uc001ujn.2	+						EP400_uc001ujl.2_Intron|EP400_uc001ujm.2_Intron|EP400_uc001ujp.2_Intron	NM_015409	NP_056224			E1A binding protein p400						histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nuclear speck	ATP binding|DNA binding|helicase activity			central_nervous_system(4)|ovary(3)|breast(3)|skin(2)	12	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	132999557	132999560	+	IGR	DEL	TCTC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132999557_132999560delTCTC								GALNT9 (93652 upstream) : FBRSL1 (67597 downstream)																																			---	---	---	---
POLE	5426	broad.mit.edu	37	12	133262465	133262466	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133262465_133262466delTT	uc001uks.1	-						POLE_uc010tbq.1_Intron|POLE_uc009zyu.1_Intron|PXMP2_uc001ukt.2_5'Flank|PGAM5_uc010tbr.1_5'Flank	NM_006231	NP_006222			DNA-directed DNA polymerase epsilon						base-excision repair, gap-filling|DNA synthesis involved in DNA repair|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	chromatin binding|DNA binding|DNA-directed DNA polymerase activity|nucleotide binding|protein binding|zinc ion binding			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)									DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
Unknown	0	broad.mit.edu	37	12	133299638	133299638	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133299638delA								PGAM5 (1723 upstream) : ANKLE2 (2616 downstream)																																			---	---	---	---
ANKLE2	23141	broad.mit.edu	37	12	133310926	133310926	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133310926delG	uc001ukx.2	-						ANKLE2_uc009zyw.1_Intron|ANKLE2_uc001uky.3_Intron	NM_015114	NP_055929			ankyrin repeat and LEM domain containing 2							cytoplasm|integral to membrane|nuclear envelope					0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	133702170	133702170	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133702170delA								ZNF140 (17914 upstream) : ZNF10 (5043 downstream)																																			---	---	---	---
DKFZp686A1627	266695	broad.mit.edu	37	13	19645199	19645199	+	Intron	DEL	T	-	-	rs112500592		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19645199delT	uc001umb.1	-							NR_002801				Homo sapiens mRNA; cDNA DKFZp686A1627 (from clone DKFZp686A1627).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	19801216	19801216	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19801216delT								TUBA3C (45280 upstream) : LOC100101938 (35725 downstream)																																			---	---	---	---
MPHOSPH8	54737	broad.mit.edu	37	13	20213452	20213453	+	Intron	DEL	TT	-	-	rs76626872		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20213452_20213453delTT	uc001umh.2	+						MPHOSPH8_uc001umf.1_Intron|MPHOSPH8_uc001umg.2_Intron	NM_017520	NP_059990			M-phase phosphoprotein 8						cell cycle	cytoplasm|nucleus					0		all_cancers(29;2.83e-16)|all_lung(29;1.16e-17)|all_epithelial(30;8.13e-16)|Lung NSC(5;6.91e-15)|Lung SC(185;0.0367)		all cancers(112;8.43e-05)|Epithelial(112;0.000426)|OV - Ovarian serous cystadenocarcinoma(117;0.00596)|Lung(94;0.015)|LUSC - Lung squamous cell carcinoma(192;0.0795)														---	---	---	---
PSPC1	55269	broad.mit.edu	37	13	20270045	20270045	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20270045delA	uc001umj.1	-						PSPC1_uc001umk.1_Intron	NM_001042414				paraspeckle protein 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nuclear matrix|nucleolus	nucleotide binding|protein binding|RNA binding			breast(1)	1		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	20506787	20506787	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20506787delA								ZMYM5 (69011 upstream) : ZMYM2 (26023 downstream)																																			---	---	---	---
ZMYM2	7750	broad.mit.edu	37	13	20629938	20629938	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20629938delT	uc001umr.2	+						ZMYM2_uc001ums.2_Intron|ZMYM2_uc001umt.2_Intron|ZMYM2_uc010tco.1_Intron|ZMYM2_uc001umv.2_Intron|ZMYM2_uc001umw.2_Intron	NM_003453	NP_003444			zinc finger protein 198						regulation of transcription, DNA-dependent|transcription, DNA-dependent	PML body	ubiquitin conjugating enzyme binding|zinc ion binding			lung(3)|ovary(2)|prostate(1)	6		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)														---	---	---	---
IFT88	8100	broad.mit.edu	37	13	21166616	21166617	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21166616_21166617delTT	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)														---	---	---	---
IFT88	8100	broad.mit.edu	37	13	21202340	21202340	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21202340delT	uc001unh.2	+						IFT88_uc001uni.2_Intron|IFT88_uc001unj.2_Intron|IFT88_uc010tcq.1_Intron|IFT88_uc001unk.2_Intron|IFT88_uc001unl.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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	22352353	22352354	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22352353_22352354delAA								FGF9 (73713 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	22545683	22545684	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22545683_22545684delTG								FGF9 (267043 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	22555012	22555013	+	IGR	INS	-	TCTCCCTG	TCTCCCTG	rs145885206	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22555012_22555013insTCTCCCTG								FGF9 (276372 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	22640964	22640964	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22640964delT	uc001uoi.2	+											Homo sapiens cDNA FLJ30283 fis, clone BRACE2002807.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	22678400	22678400	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22678400delT	uc001uoi.2	+											Homo sapiens cDNA FLJ30283 fis, clone BRACE2002807.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	23507701	23507704	+	IGR	DEL	CAAC	-	-	rs148908652	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23507701_23507704delCAAC								None (None upstream) : SGCG (247356 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	24302456	24302457	+	IGR	INS	-	AAAC	AAAC	rs145661970	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24302456_24302457insAAAC								TNFRSF19 (52225 upstream) : MIPEP (1872 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	24541356	24541356	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24541356delT								C1QTNF9B (69715 upstream) : SPATA13 (12483 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	25679295	25679295	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25679295delA								PABPC3 (6593 upstream) : FAM123A (63378 downstream)																																			---	---	---	---
ATP8A2	51761	broad.mit.edu	37	13	25955028	25955028	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25955028delA	uc001uqk.2	+							NM_016529	NP_057613			ATPase, aminophospholipid transporter-like,						ATP biosynthetic process|negative regulation of cell proliferation	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|large_intestine(1)|skin(1)	4		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)														---	---	---	---
CDK8	1024	broad.mit.edu	37	13	26892446	26892446	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26892446delA	uc001uqr.1	+						CDK8_uc001uqs.1_Intron|CDK8_uc001uqt.1_Intron	NM_001260	NP_001251			cyclin-dependent kinase 8						regulation of transcription, DNA-dependent|transcription, DNA-dependent	mediator complex	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity			lung(2)|large_intestine(1)|ovary(1)|skin(1)	5	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0384)|Epithelial(112;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.188)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	27106704	27106705	+	IGR	INS	-	CT	CT	rs143252803	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27106704_27106705insCT								CDK8 (128135 upstream) : WASF3 (25135 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	27402596	27402598	+	IGR	DEL	TTT	-	-	rs66538815		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27402596_27402598delTTT								GPR12 (67674 upstream) : USP12 (239840 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	27435500	27435500	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27435500delT								GPR12 (100578 upstream) : USP12 (206938 downstream)																																			---	---	---	---
RPL21	6144	broad.mit.edu	37	13	27830671	27830671	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27830671delA	uc001ura.2	+	6						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)														---	---	---	---
PAN3	255967	broad.mit.edu	37	13	28767874	28767881	+	Intron	DEL	AAAAAAAA	-	-	rs67890244		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28767874_28767881delAAAAAAAA	uc001urz.2	+						PAN3_uc010tdo.1_Intron|PAN3_uc001ury.2_Intron|PAN3_uc001urx.2_Intron	NM_175854	NP_787050			PABP1-dependent poly A-specific ribonuclease						nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening	centrosome|cytosol	ATP binding|protein kinase activity			ovary(1)	1	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)	Colorectal(13;0.000334)	all cancers(112;0.0102)|Epithelial(112;0.0803)|GBM - Glioblastoma multiforme(144;0.121)|OV - Ovarian serous cystadenocarcinoma(117;0.13)|Lung(94;0.174)														---	---	---	---
FLT1	2321	broad.mit.edu	37	13	28925155	28925155	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28925155delT	uc001usb.3	-							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	29385354	29385354	+	IGR	DEL	A	-	-	rs72038200		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29385354delA								SLC46A3 (92204 upstream) : MTUS2 (213394 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	30243405	30243405	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30243405delA								SLC7A1 (73580 upstream) : UBL3 (95141 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	30463766	30463767	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30463766_30463767insA								UBL3 (38946 upstream) : KATNAL1 (313001 downstream)																																			---	---	---	---
KATNAL1	84056	broad.mit.edu	37	13	30795056	30795057	+	Intron	INS	-	C	C	rs142814326	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30795056_30795057insC	uc001uss.2	-						KATNAL1_uc001ust.2_Intron	NM_001014380	NP_001014402			katanin p60 subunit A-like 1							cytoplasm|microtubule	ATP binding|microtubule-severing ATPase activity				0		Lung SC(185;0.0257)		all cancers(112;0.114)|OV - Ovarian serous cystadenocarcinoma(117;0.213)														---	---	---	---
HMGB1	3146	broad.mit.edu	37	13	31036852	31036852	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31036852delA	uc001usw.2	-						HMGB1_uc001usz.2_Intron|HMGB1_uc001usv.2_Intron|HMGB1_uc001usx.2_Intron|HMGB1_uc001usy.2_Intron|HMGB1_uc001uta.1_Intron	NM_002128	NP_002119			high-mobility group box 1						base-excision repair, DNA ligation|dendritic cell chemotaxis|DNA fragmentation involved in apoptotic nuclear change|DNA topological change|inflammatory response to antigenic stimulus|innate immune response|myeloid dendritic cell activation|negative regulation of RNA polymerase II transcriptional preinitiation complex assembly|neuron projection development|positive regulation of apoptosis|positive regulation of caspase activity|positive regulation of DNA binding|positive regulation of transcription from RNA polymerase II promoter|V(D)J recombination	cell surface|condensed chromosome|extracellular space|nucleolus|nucleoplasm	chemoattractant activity|cytokine activity|damaged DNA binding|DNA bending activity|double-stranded DNA binding|RAGE receptor binding|repressing transcription factor binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding			ovary(1)	1		Lung SC(185;0.0257)		all cancers(112;0.072)|OV - Ovarian serous cystadenocarcinoma(117;0.177)|Lung(94;0.216)|GBM - Glioblastoma multiforme(144;0.232)														---	---	---	---
HSPH1	10808	broad.mit.edu	37	13	31715454	31715454	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31715454delA	uc001utj.2	-						HSPH1_uc001utk.2_Intron|HSPH1_uc010aaw.2_Intron|HSPH1_uc001utl.2_Intron|HSPH1_uc010tds.1_Intron	NM_006644	NP_006635			heat shock 105kD						positive regulation of MHC class I biosynthetic process|positive regulation of NK T cell activation|response to unfolded protein	cytoplasm|extracellular region	ATP binding				0		Lung SC(185;0.0257)		all cancers(112;0.00385)|Epithelial(112;0.0328)|OV - Ovarian serous cystadenocarcinoma(117;0.0375)|GBM - Glioblastoma multiforme(144;0.125)														---	---	---	---
EEF1DP3	196549	broad.mit.edu	37	13	32426238	32426239	+	Intron	INS	-	G	G	rs111720409		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32426238_32426239insG	uc001utu.2	+						EEF1DP3_uc010tdv.1_Intron					Homo sapiens similar to hypothetical protein FLJ20897, mRNA (cDNA clone IMAGE:5267252).												0																		---	---	---	---
FRY	10129	broad.mit.edu	37	13	32698727	32698727	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32698727delT	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)														---	---	---	---
N4BP2L1	90634	broad.mit.edu	37	13	32987256	32987256	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32987256delT	uc001uuc.2	-						N4BP2L1_uc001uud.2_Intron|N4BP2L1_uc010tdy.1_Intron|N4BP2L1_uc001uuf.2_Intron	NM_052818	NP_438169			NEDD4 binding protein 2-like 1 isoform 1						cell killing		ATP binding			ovary(1)	1		Lung SC(185;0.0262)		all cancers(112;6.3e-06)|Epithelial(112;3.51e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00607)|BRCA - Breast invasive adenocarcinoma(63;0.0171)														---	---	---	---
PDS5B	23047	broad.mit.edu	37	13	33197845	33197845	+	Intron	DEL	T	-	-	rs80249014		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33197845delT	uc010abf.2	+						PDS5B_uc001uun.2_Intron|PDS5B_uc001uuo.2_Intron|PDS5B_uc010abg.2_Intron	NM_015032	NP_055847			PDS5, regulator of cohesion maintenance, homolog						cell division|cell proliferation|mitotic sister chromatid cohesion|negative regulation of cell proliferation	chromatin|nucleus	ATP binding|DNA binding|identical protein binding			ovary(2)|lung(1)|pancreas(1)	4		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	33372657	33372657	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33372657delT								PDS5B (20502 upstream) : KL (217544 downstream)																																			---	---	---	---
KL	9365	broad.mit.edu	37	13	33633618	33633618	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33633618delT	uc001uus.2	+						KL_uc001uur.1_Intron	NM_004795	NP_004786			klotho precursor						aging|carbohydrate metabolic process|insulin receptor signaling pathway|positive regulation of bone mineralization	extracellular space|extracellular space|integral to membrane|integral to plasma membrane|membrane fraction|soluble fraction	beta-glucosidase activity|beta-glucuronidase activity|cation binding|fibroblast growth factor binding|hormone activity|signal transducer activity|vitamin D binding			large_intestine(1)|ovary(1)|skin(1)	3	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)														---	---	---	---
STARD13	90627	broad.mit.edu	37	13	33824314	33824314	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33824314delA	uc001uuw.2	-						STARD13_uc001uux.2_Intron|STARD13_uc010tec.1_Intron|STARD13_uc010abh.1_Intron	NM_178006	NP_821074			StAR-related lipid transfer (START) domain						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|lipid particle|mitochondrial membrane	GTPase activator activity|protein binding			ovary(2)|pancreas(1)|skin(1)	4	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)														---	---	---	---
STARD13	90627	broad.mit.edu	37	13	33957516	33957516	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33957516delA	uc001uux.2	-							NM_052851	NP_443083			StAR-related lipid transfer (START) domain						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|lipid particle|mitochondrial membrane	GTPase activator activity|protein binding			ovary(2)|pancreas(1)|skin(1)	4	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	34607723	34607723	+	IGR	DEL	T	-	-	rs67105144		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34607723delT								RFC3 (67029 upstream) : NBEA (908733 downstream)																																			---	---	---	---
NBEA	26960	broad.mit.edu	37	13	35569751	35569752	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35569751_35569752insA	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	35700128	35700128	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35700128delA	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	35838124	35838124	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35838124delT	uc001uvb.2	+						NBEA_uc010abi.2_Intron	NM_015678	NP_056493			neurobeachin							cytosol|endomembrane system|plasma membrane|trans-Golgi network	protein binding			ovary(9)|large_intestine(2)	11		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)														---	---	---	---
NBEA	26960	broad.mit.edu	37	13	36115420	36115420	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36115420delT	uc001uvb.2	+						NBEA_uc010abi.2_Intron|NBEA_uc010tee.1_Intron|NBEA_uc010tef.1_Intron|NBEA_uc010teg.1_Intron	NM_015678	NP_056493			neurobeachin							cytosol|endomembrane system|plasma membrane|trans-Golgi network	protein binding			ovary(9)|large_intestine(2)	11		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)														---	---	---	---
NBEA	26960	broad.mit.edu	37	13	36242470	36242470	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36242470delT	uc001uvb.2	+						NBEA_uc010abi.2_Intron|NBEA_uc010tef.1_Intron|NBEA_uc001uvd.2_Intron	NM_015678	NP_056493			neurobeachin							cytosol|endomembrane system|plasma membrane|trans-Golgi network	protein binding			ovary(9)|large_intestine(2)	11		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)														---	---	---	---
FAM48A	55578	broad.mit.edu	37	13	37605615	37605615	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37605615delT	uc001uwg.2	-						FAM48A_uc010abt.2_Intron|FAM48A_uc001uwh.2_Intron|FAM48A_uc001uwi.2_Intron|FAM48A_uc001uwj.2_Intron|FAM48A_uc001uwk.2_Intron|FAM48A_uc010tes.1_Intron|FAM48A_uc001uwl.1_Intron	NM_001014286	NP_001014308			family with sequence similarity 48, member A						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	38171302	38171302	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38171302delA	uc001uwo.3	-						POSTN_uc001uwp.3_Intron|POSTN_uc001uwr.2_Intron|POSTN_uc001uwq.2_Intron|POSTN_uc010teu.1_Intron|POSTN_uc010tev.1_Intron|POSTN_uc010tew.1_Intron|POSTN_uc010tex.1_Intron	NM_006475	NP_006466			periostin, osteoblast specific factor isoform 1						cell adhesion|skeletal system development	proteinaceous extracellular matrix	heparin binding			ovary(2)	2		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	38967021	38967021	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38967021delT								UFM1 (29879 upstream) : FREM2 (294152 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	39095523	39095525	+	IGR	DEL	AAA	-	-	rs34637746		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39095523_39095525delAAA								UFM1 (158381 upstream) : FREM2 (165648 downstream)																																			---	---	---	---
FREM2	341640	broad.mit.edu	37	13	39331729	39331729	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39331729delT	uc001uwv.2	+							NM_207361	NP_997244			FRAS1-related extracellular matrix protein 2						cell communication|homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(7)|pancreas(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	11		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)														---	---	---	---
FREM2	341640	broad.mit.edu	37	13	39395404	39395404	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39395404delT	uc001uwv.2	+						FREM2_uc001uww.2_Intron	NM_207361	NP_997244			FRAS1-related extracellular matrix protein 2						cell communication|homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(7)|pancreas(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	11		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	39625530	39625530	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39625530delT								NHLRC3 (1288 upstream) : LHFP (291500 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	39832582	39832582	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39832582delT								NHLRC3 (208340 upstream) : LHFP (84448 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	40419662	40419663	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40419662_40419663insT								COG6 (53860 upstream) : LOC646982 (501610 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	40460992	40460992	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40460992delA								COG6 (95190 upstream) : LOC646982 (460281 downstream)																																			---	---	---	---
FOXO1	2308	broad.mit.edu	37	13	41078284	41078285	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41078284_41078285delAC	uc010acc.1	-							NM_002015	NP_002006			forkhead box O1						anti-apoptosis|blood vessel development|embryo development|endocrine pancreas development|insulin receptor signaling pathway|negative regulation of stress-activated MAPK cascade|nerve growth factor receptor signaling pathway|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|response to DNA damage stimulus|tissue development	cytosol|transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding		PAX3/FOXO1(749)|PAX7/FOXO1(197)	soft_tissue(946)|lung(1)|central_nervous_system(1)	948		Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815)														---	---	---	---
KIAA0564	23078	broad.mit.edu	37	13	42249231	42249231	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42249231delA	uc001uyj.2	-							NM_015058	NP_055873			hypothetical protein LOC23078 isoform a							extracellular region	ATP binding|ATPase activity			ovary(3)|upper_aerodigestive_tract(1)|kidney(1)|skin(1)	6		Lung NSC(96;4.61e-06)|Prostate(109;0.0167)|Lung SC(185;0.0262)|Breast(139;0.0854)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000368)|GBM - Glioblastoma multiforme(144;0.0033)|BRCA - Breast invasive adenocarcinoma(63;0.0969)														---	---	---	---
KIAA0564	23078	broad.mit.edu	37	13	42302298	42302298	+	Intron	DEL	T	-	-	rs9562343	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42302298delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	42544062	42544062	+	IGR	DEL	T	-	-	rs78568043		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42544062delT								KIAA0564 (8841 upstream) : DGKH (70110 downstream)																																			---	---	---	---
DGKH	160851	broad.mit.edu	37	13	42712501	42712502	+	Intron	DEL	GA	-	-	rs67550655		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42712501_42712502delGA	uc001uyl.1	+						DGKH_uc010tfh.1_Intron|DGKH_uc001uym.1_Intron|DGKH_uc010tfi.1_Intron|DGKH_uc010tfj.1_Intron|DGKH_uc001uyn.1_Intron|DGKH_uc001uyo.1_Intron|DGKH_uc001uyp.2_Intron	NM_178009	NP_821077			diacylglycerol kinase, eta isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation|protein oligomerization	endosome|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(2)	2		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	43570671	43570671	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43570671delT								EPSTI1 (4294 upstream) : DNAJC15 (26691 downstream)																																			---	---	---	---
ZC3H13	23091	broad.mit.edu	37	13	46577610	46577610	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46577610delA	uc010tfw.1	-						ZC3H13_uc001vas.1_Intron|ZC3H13_uc001vat.1_Intron	NM_015070	NP_055885			zinc finger CCCH-type containing 13								nucleic acid binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(96;7.26e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;4.18e-05)														---	---	---	---
C13orf18	80183	broad.mit.edu	37	13	46965385	46965386	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46965385_46965386insT	uc001vbi.3	-						C13orf18_uc001vbh.3_5'Flank	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	47459186	47459186	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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	47543392	47543393	+	IGR	DEL	TT	-	-	rs67029680		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47543392_47543393delTT								HTR2A (72342 upstream) : SUCLA2 (973399 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	47638053	47638054	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47638053_47638054insT								HTR2A (167003 upstream) : SUCLA2 (878738 downstream)																																			---	---	---	---
RB1	5925	broad.mit.edu	37	13	48899121	48899122	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48899121_48899122delTT	uc001vcb.2	+						RB1_uc010acs.1_Intron	NM_000321	NP_000312			retinoblastoma 1						androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding			lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	358		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)		6	D|Mis|N|F|S		retinoblastoma|sarcoma|breast|small cell lung	retinoblastoma|sarcoma|breast|small cell lung			Hereditary_Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			---	---	---	---
RB1	5925	broad.mit.edu	37	13	48954160	48954161	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48954160_48954161delTT	uc001vcb.2	+							NM_000321	NP_000312			retinoblastoma 1						androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding	p.?(7)		lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	358		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)		6	D|Mis|N|F|S		retinoblastoma|sarcoma|breast|small cell lung	retinoblastoma|sarcoma|breast|small cell lung			Hereditary_Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			---	---	---	---
Unknown	0	broad.mit.edu	37	13	49339083	49339084	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49339083_49339084insA								CYSLTR2 (55585 upstream) : FNDC3A (210964 downstream)																																			---	---	---	---
FNDC3A	22862	broad.mit.edu	37	13	49660022	49660031	+	Intron	DEL	TTTTTTTTTC	-	-	rs11446314		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49660022_49660031delTTTTTTTTTC	uc001vcm.2	+						FNDC3A_uc001vcl.1_Intron|FNDC3A_uc001vcn.2_Intron|FNDC3A_uc001vco.2_Intron	NM_001079673	NP_001073141			fibronectin type III domain containing 3A							Golgi membrane|integral to membrane				lung(2)	2		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)														---	---	---	---
FNDC3A	22862	broad.mit.edu	37	13	49742591	49742592	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49742591_49742592delTT	uc001vcm.2	+						FNDC3A_uc001vcn.2_Intron|FNDC3A_uc001vco.2_Intron|FNDC3A_uc001vcp.1_Intron|FNDC3A_uc001vcq.2_Intron	NM_001079673	NP_001073141			fibronectin type III domain containing 3A							Golgi membrane|integral to membrane				lung(2)	2		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	50530806	50530812	+	IGR	DEL	TTTTTTT	-	-	rs142536226		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50530806_50530812delTTTTTTT								C13orf1 (20181 upstream) : DLEU2 (25876 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	50556130	50556130	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50556130delA								C13orf1 (45505 upstream) : DLEU2 (558 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	51194156	51194156	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51194156delA	uc001vet.1	+											Homo sapiens mRNA for B-cell neoplasia associated transcript, (BCMS gene), splice variant D, non coding transcript.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	51478748	51478748	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51478748delT								DLEU7 (60863 upstream) : RNASEH2B (5144 downstream)																																			---	---	---	---
RNASEH2B	79621	broad.mit.edu	37	13	51524592	51524592	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51524592delA	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	51671885	51671885	+	IGR	DEL	T	-	-	rs113649039		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51671885delT								GUCY1B2 (16887 upstream) : FAM124A (124622 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	51767000	51767000	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51767000delA								GUCY1B2 (112002 upstream) : FAM124A (29507 downstream)																																			---	---	---	---
CKAP2	26586	broad.mit.edu	37	13	53049034	53049034	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53049034delA	uc001vgv.2	+	9	2007	c.1810delA	c.(1810-1812)AAAfs	p.K604fs	CKAP2_uc001vgu.2_Frame_Shift_Del_p.K603fs|CKAP2_uc010tha.1_Frame_Shift_Del_p.K555fs	NM_001098525	NP_001091995	Q8WWK9	CKAP2_HUMAN	cytoskeleton associated protein 2 isoform 2	604					apoptosis|cell cycle	centrosome|microtubule|spindle pole				ovary(1)|skin(1)	2		Breast(56;0.000207)|Lung NSC(96;0.00212)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.6e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	53448576	53448577	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53448576_53448577delTT								PCDH8 (25802 upstream) : OLFM4 (154395 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	54418177	54418177	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:54418177delT								OLFM4 (791991 upstream) : MIR1297 (467930 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	55469439	55469439	+	IGR	DEL	T	-	-	rs76611342		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:55469439delT								MIR1297 (583256 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	56003479	56003479	+	IGR	DEL	T	-	-	rs79908254		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:56003479delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	56524958	56524958	+	IGR	DEL	A	-	-	rs142906653		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:56524958delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	57703448	57703449	+	IGR	DEL	AA	-	-	rs75858143		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:57703448_57703449delAA								None (None upstream) : PRR20C (11603 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	58374265	58374265	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58374265delT								PCDH17 (71200 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	59076545	59076546	+	IGR	DEL	TT	-	-	rs77263897	byFrequency;by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:59076545_59076546delTT								PCDH17 (773480 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	59188768	59188772	+	IGR	DEL	GAAAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:59188768_59188772delGAAAA								PCDH17 (885703 upstream) : None (None downstream)																																			---	---	---	---
DIAPH3	81624	broad.mit.edu	37	13	60361079	60361079	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60361079delA	uc001vht.2	-						DIAPH3_uc001vhu.2_Intron	NM_001042517	NP_001035982			diaphanous homolog 3 isoform a						actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)	2		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	60909898	60909901	+	IGR	DEL	ATTT	-	-	rs34959054		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60909898_60909901delATTT								DIAPH3 (171779 upstream) : TDRD3 (60690 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	60951943	60951943	+	IGR	DEL	A	-	-	rs145012076		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60951943delA								DIAPH3 (213824 upstream) : TDRD3 (18648 downstream)																																			---	---	---	---
TDRD3	81550	broad.mit.edu	37	13	61043570	61043571	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61043570_61043571delAC	uc001via.2	+						TDRD3_uc010aef.2_Intron|TDRD3_uc001vhz.3_Intron|TDRD3_uc010aeg.2_Intron|TDRD3_uc001vib.3_Intron	NM_030794	NP_110421			tudor domain containing 3 isoform 2						chromatin modification	cytoplasm|nucleus	chromatin binding|methylated histone residue binding|nucleic acid binding|transcription coactivator activity			upper_aerodigestive_tract(1)|skin(1)	2		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)														---	---	---	---
TDRD3	81550	broad.mit.edu	37	13	61057789	61057789	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61057789delT	uc001via.2	+						TDRD3_uc010aef.2_Intron|TDRD3_uc001vhz.3_Intron|TDRD3_uc010aeg.2_Intron|TDRD3_uc001vib.3_Intron	NM_030794	NP_110421			tudor domain containing 3 isoform 2						chromatin modification	cytoplasm|nucleus	chromatin binding|methylated histone residue binding|nucleic acid binding|transcription coactivator activity			upper_aerodigestive_tract(1)|skin(1)	2		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)														---	---	---	---
TDRD3	81550	broad.mit.edu	37	13	61141862	61141862	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61141862delT	uc001via.2	+						TDRD3_uc001vhz.3_Intron|TDRD3_uc010aeg.2_Intron|TDRD3_uc001vib.3_Intron	NM_030794	NP_110421			tudor domain containing 3 isoform 2						chromatin modification	cytoplasm|nucleus	chromatin binding|methylated histone residue binding|nucleic acid binding|transcription coactivator activity			upper_aerodigestive_tract(1)|skin(1)	2		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	61592125	61592126	+	IGR	DEL	CA	-	-	rs35231861		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61592125_61592126delCA								TDRD3 (444113 upstream) : PCDH20 (391695 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	62433650	62433650	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:62433650delA								PCDH20 (431571 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	62692332	62692333	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:62692332_62692333delAC								PCDH20 (690253 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	63399486	63399486	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63399486delA								None (None upstream) : OR7E156P (912082 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	63642627	63642628	+	IGR	INS	-	TGCT	TGCT	rs138889651	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63642627_63642628insTGCT								None (None upstream) : OR7E156P (668940 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	63705213	63705213	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63705213delT								None (None upstream) : OR7E156P (606355 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	63976118	63976121	+	IGR	DEL	TTCC	-	-	rs111579679		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63976118_63976121delTTCC								None (None upstream) : OR7E156P (335447 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	65078599	65078599	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:65078599delT								OR7E156P (761898 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	65950244	65950244	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:65950244delA								None (None upstream) : PCDH9 (926723 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	68738232	68738232	+	IGR	DEL	T	-	-	rs149473115	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68738232delT								PCDH9 (933764 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	70808355	70808355	+	IGR	DEL	A	-	-	rs76397604		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:70808355delA								ATXN8OS (94470 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	70944092	70944092	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:70944092delT								ATXN8OS (230207 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	71159273	71159274	+	IGR	INS	-	TG	TG	rs143158349	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71159273_71159274insTG								ATXN8OS (445388 upstream) : DACH1 (852824 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	71722437	71722437	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71722437delA								None (None upstream) : DACH1 (289661 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	71918490	71918490	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71918490delT								None (None upstream) : DACH1 (93608 downstream)																																			---	---	---	---
DACH1	1602	broad.mit.edu	37	13	72131053	72131053	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72131053delT	uc010thn.1	-						DACH1_uc010tho.1_Intron|DACH1_uc010thp.1_Intron	NM_080759	NP_542937			dachshund homolog 1 isoform a						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|nucleotide binding|protein binding			breast(1)	1		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	72483035	72483035	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72483035delT								DACH1 (41705 upstream) : C13orf37 (799460 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	72517459	72517459	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72517459delT								DACH1 (76129 upstream) : C13orf37 (765036 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	72600234	72600235	+	IGR	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72600234_72600235delGT								DACH1 (158904 upstream) : C13orf37 (682260 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	73041135	73041135	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73041135delC								DACH1 (599805 upstream) : C13orf37 (241360 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	73042480	73042480	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73042480delT								DACH1 (601150 upstream) : C13orf37 (240015 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	73623333	73623334	+	IGR	INS	-	T	T	rs147637307	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73623333_73623334insT								PIBF1 (32744 upstream) : KLF5 (5780 downstream)																																			---	---	---	---
KLF5	688	broad.mit.edu	37	13	73637032	73637033	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73637032_73637033delTT	uc001vje.2	+						KLF5_uc001vjd.2_Intron	NM_001730	NP_001721			Kruppel-like factor 5						transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)|pancreas(1)	3		Prostate(6;0.00187)|Breast(118;0.0735)		GBM - Glioblastoma multiforme(99;0.0011)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	73668500	73668501	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73668500_73668501insA								KLF5 (16825 upstream) : KLF12 (591649 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	73966306	73966309	+	IGR	DEL	AAAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73966306_73966309delAAAA								KLF5 (314631 upstream) : KLF12 (293841 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	74828397	74828397	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74828397delA	uc001vji.1	+											Homo sapiens cDNA FLJ32127 fis, clone PEBLM2000126.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	75658347	75658348	+	IGR	DEL	GA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75658347_75658348delGA								KLF12 (949953 upstream) : LOC647288 (153542 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	76950543	76950543	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76950543delT								LMO7 (516539 upstream) : KCTD12 (503761 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	77423327	77423327	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77423327delA								LMO7 (989323 upstream) : KCTD12 (30977 downstream)																																			---	---	---	---
MYCBP2	23077	broad.mit.edu	37	13	77834802	77834803	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77834802_77834803delAA	uc001vkf.2	-						MYCBP2_uc010aev.2_Intron	NM_015057	NP_055872			MYC binding protein 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	78611574	78611575	+	Intron	DEL	TT	-	-	rs75962320		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78611574_78611575delTT	uc001vks.2	+											Homo sapiens cDNA FLJ38460 fis, clone FEBRA2020801.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	80636002	80636003	+	IGR	INS	-	AT	AT	rs9645962		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80636002_80636003insAT								NDFIP2 (505797 upstream) : SPRY2 (274111 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	80747188	80747188	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80747188delA								NDFIP2 (616983 upstream) : SPRY2 (162926 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	80827692	80827692	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80827692delA								NDFIP2 (697487 upstream) : SPRY2 (82422 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	80896552	80896553	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80896552_80896553delAA								NDFIP2 (766347 upstream) : SPRY2 (13561 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	80991785	80991785	+	IGR	DEL	T	-	-	rs76652403		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80991785delT								SPRY2 (76699 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	81042923	81042924	+	IGR	DEL	TG	-	-	rs68027559		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81042923_81042924delTG								SPRY2 (127837 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	83478294	83478295	+	IGR	INS	-	AC	AC	rs146343855	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83478294_83478295insAC								None (None upstream) : SLITRK1 (973049 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	85150501	85150502	+	IGR	INS	-	AG	AG	rs142299312	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:85150501_85150502insAG								SLITRK1 (693973 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	85195629	85195629	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:85195629delT								SLITRK1 (739101 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	86151205	86151206	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:86151205_86151206insA								None (None upstream) : SLITRK6 (215716 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	86706316	86706317	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:86706316_86706317delTT								SLITRK6 (332833 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	88516843	88516843	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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	88542299	88542299	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88542299delT								SLITRK5 (210431 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	88701154	88701154	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88701154delA								SLITRK5 (369286 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	88836232	88836232	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88836232delA								SLITRK5 (504364 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	89133562	89133562	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89133562delT								SLITRK5 (801694 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	89451769	89451769	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89451769delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	89673363	89673367	+	IGR	DEL	TTTTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89673363_89673367delTTTTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	90873771	90873771	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:90873771delA								None (None upstream) : MIR622 (9665 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	91421827	91421827	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:91421827delA								MIR622 (538296 upstream) : LOC144776 (121381 downstream)																																			---	---	---	---
GPC5	2262	broad.mit.edu	37	13	92368504	92368504	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92368504delT	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	93274819	93274820	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93274819_93274820delTT	uc010tif.1	+							NM_004466	NP_004457			glypican 5 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			ovary(2)|skin(2)|upper_aerodigestive_tract(1)	5	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)																---	---	---	---
Unknown	0	broad.mit.edu	37	13	93724342	93724342	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93724342delA								GPC5 (204857 upstream) : GPC6 (154736 downstream)																																			---	---	---	---
GPC6	10082	broad.mit.edu	37	13	94073969	94073969	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94073969delA	uc001vlt.2	+						GPC6_uc010tig.1_Intron	NM_005708	NP_005699			glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)																---	---	---	---
GPC6	10082	broad.mit.edu	37	13	94293162	94293162	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94293162delT	uc001vlt.2	+						GPC6_uc010tig.1_Intron|GPC6_uc001vlu.1_Intron	NM_005708	NP_005699			glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)																---	---	---	---
GPC6	10082	broad.mit.edu	37	13	94425710	94425710	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94425710delT	uc001vlt.2	+						GPC6_uc010tig.1_Intron|GPC6_uc001vlu.1_Intron	NM_005708	NP_005699			glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)																---	---	---	---
GPC6	10082	broad.mit.edu	37	13	94482866	94482875	+	Intron	DEL	AAAAAAAAAA	-	-	rs34601053		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94482866_94482875delAAAAAAAAAA	uc001vlt.2	+						GPC6_uc010tig.1_Intron|GPC6_uc001vlu.1_3'UTR	NM_005708	NP_005699			glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)																---	---	---	---
GPC6	10082	broad.mit.edu	37	13	94982076	94982076	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94982076delA	uc001vlt.2	+							NM_005708	NP_005699			glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)																---	---	---	---
GPC6	10082	broad.mit.edu	37	13	94989046	94989046	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94989046delA	uc001vlt.2	+							NM_005708	NP_005699			glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)																---	---	---	---
TGDS	23483	broad.mit.edu	37	13	95233266	95233266	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95233266delA	uc001vlw.2	-						TGDS_uc001vlx.2_Intron	NM_014305	NP_055120			TDP-glucose 4,6-dehydratase						cellular metabolic process		coenzyme binding|dTDP-glucose 4,6-dehydratase activity|protein binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)																	---	---	---	---
GPR180	160897	broad.mit.edu	37	13	95273596	95273596	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95273596delT	uc001vly.2	+						GPR180_uc001vlz.2_Intron|GPR180_uc010afi.2_Intron	NM_180989	NP_851320			G protein-coupled receptor 180 precursor							integral to membrane				breast(1)	1	all_neural(89;0.0684)|Medulloblastoma(90;0.163)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	95402102	95402105	+	IGR	DEL	CTCT	-	-	rs71111549		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95402102_95402105delCTCT								SOX21 (37713 upstream) : ABCC4 (269979 downstream)																																			---	---	---	---
ABCC4	10257	broad.mit.edu	37	13	95696129	95696129	+	Intron	DEL	A	-	-	rs4148539		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95696129delA	uc001vmd.3	-						ABCC4_uc010afj.2_Intron|ABCC4_uc010afk.2_Intron	NM_005845	NP_005836			ATP-binding cassette, sub-family C, member 4						platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			central_nervous_system(3)|skin(1)	4	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)													---	---	---	---
ABCC4	10257	broad.mit.edu	37	13	95714849	95714849	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95714849delA	uc001vmd.3	-						ABCC4_uc010afj.2_Intron|ABCC4_uc010afk.2_Intron	NM_005845	NP_005836			ATP-binding cassette, sub-family C, member 4						platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			central_nervous_system(3)|skin(1)	4	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)													---	---	---	---
ABCC4	10257	broad.mit.edu	37	13	95748443	95748443	+	Intron	DEL	A	-	-	rs75002273		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95748443delA	uc001vmd.3	-						ABCC4_uc010afk.2_Intron|ABCC4_uc001vme.2_Intron|ABCC4_uc010tih.1_Intron	NM_005845	NP_005836			ATP-binding cassette, sub-family C, member 4						platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			central_nervous_system(3)|skin(1)	4	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)													---	---	---	---
CLDN10	9071	broad.mit.edu	37	13	96208307	96208307	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96208307delT	uc001vmh.2	+						CLDN10_uc001vmg.2_Intron|CLDN10_uc010tii.1_Intron	NM_006984	NP_008915			claudin 10 isoform b						calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity			ovary(1)	1	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.18)															---	---	---	---
DNAJC3	5611	broad.mit.edu	37	13	96443359	96443359	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96443359delA	uc001vmq.2	+	12					DNAJC3_uc001vmr.2_3'UTR	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)															---	---	---	---
UGGT2	55757	broad.mit.edu	37	13	96512945	96512945	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96512945delT	uc001vmt.2	-							NM_020121	NP_064506			UDP-glucose ceramide glucosyltransferase-like 2						post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	96724689	96724689	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96724689delT								UGGT2 (18953 upstream) : HS6ST3 (18404 downstream)																																			---	---	---	---
HS6ST3	266722	broad.mit.edu	37	13	97418030	97418030	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97418030delT	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	97700081	97700081	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97700081delA								OXGR1 (53477 upstream) : MBNL2 (174493 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	97869098	97869099	+	IGR	INS	-	TG	TG	rs144463675	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97869098_97869099insTG								OXGR1 (222494 upstream) : MBNL2 (5475 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	98458576	98458578	+	IGR	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98458576_98458578delAAA								RAP2A (338325 upstream) : IPO5 (147351 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	98546132	98546132	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98546132delA								RAP2A (425881 upstream) : IPO5 (59797 downstream)																																			---	---	---	---
IPO5	3843	broad.mit.edu	37	13	98638369	98638369	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98638369delA	uc001vnf.1	+						IPO5_uc001vne.2_Intron|IPO5_uc010tik.1_Intron|IPO5_uc010til.1_Intron	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	98658181	98658181	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98658181delA	uc001vnf.1	+						IPO5_uc001vne.2_Intron|IPO5_uc010tik.1_Intron|IPO5_uc010til.1_Intron|IPO5_uc001vng.1_Intron	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	98710148	98710149	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98710148_98710149delAA								IPO5 (33599 upstream) : FARP1 (84667 downstream)																																			---	---	---	---
STK24	8428	broad.mit.edu	37	13	99213159	99213162	+	Intron	DEL	AAAA	-	-	rs112490356		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99213159_99213162delAAAA	uc001vnn.1	-						STK24_uc010tim.1_Intron	NM_001032296	NP_001027467			serine/threonine kinase 24 isoform b						cellular component disassembly involved in apoptosis|signal transduction	cytosol|nucleoplasm	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)|lung(1)	2	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)															---	---	---	---
Unknown	0	broad.mit.edu	37	13	100104836	100104837	+	IGR	INS	-	TT	TT			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100104836_100104837insTT								UBAC2 (66085 upstream) : TM9SF2 (48891 downstream)																																			---	---	---	---
CLYBL	171425	broad.mit.edu	37	13	100273046	100273047	+	Intron	INS	-	AAAG	AAAG	rs147732033	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100273046_100273047insAAAG	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	100425014	100425014	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100425014delT	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	100542514	100542514	+	Intron	DEL	T	-	-	rs79505258		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100542514delT	uc001vok.2	+							NM_206808	NP_996531			citrate lyase beta like precursor						cellular aromatic compound metabolic process	citrate lyase complex|mitochondrion	citrate (pro-3S)-lyase activity|metal ion binding				0	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	100597549	100597550	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100597549_100597550insA								CLYBL (52726 upstream) : ZIC5 (17725 downstream)																																			---	---	---	---
PCCA	5095	broad.mit.edu	37	13	101001185	101001188	+	Intron	DEL	TTTC	-	-	rs72503659		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101001185_101001188delTTTC	uc001voo.2	+						PCCA_uc010aga.2_Intron|PCCA_uc010tiz.1_Intron|PCCA_uc001vop.2_Intron	NM_000282	NP_000273			propionyl-Coenzyme A carboxylase, alpha						fatty acid beta-oxidation	mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|enzyme binding|metal ion binding|propionyl-CoA carboxylase activity			skin(2)	2	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)													---	---	---	---
PCCA	5095	broad.mit.edu	37	13	101032454	101032454	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101032454delA	uc001voo.2	+						PCCA_uc010aga.2_Intron|PCCA_uc010tiz.1_Intron|PCCA_uc001vop.2_Intron	NM_000282	NP_000273			propionyl-Coenzyme A carboxylase, alpha						fatty acid beta-oxidation	mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|enzyme binding|metal ion binding|propionyl-CoA carboxylase activity			skin(2)	2	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)													---	---	---	---
NALCN	259232	broad.mit.edu	37	13	101838245	101838245	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101838245delT	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)																	---	---	---	---
NALCN	259232	broad.mit.edu	37	13	101952752	101952755	+	Intron	DEL	TCCT	-	-	rs67198400	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101952752_101952755delTCCT	uc001vox.1	-						NALCN_uc001voy.2_Intron|NALCN_uc001voz.2_Intron|NALCN_uc001vpa.2_Intron	NM_052867	NP_443099			voltage gated channel like 1							integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
ITGBL1	9358	broad.mit.edu	37	13	102174189	102174189	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102174189delT	uc001vpb.2	+						ITGBL1_uc010agb.2_Intron|ITGBL1_uc001vpc.3_Intron	NM_004791	NP_004782			integrin, beta-like 1 (with EGF-like repeat						cell-matrix adhesion|integrin-mediated signaling pathway	extracellular region|integrin complex	binding|receptor activity			ovary(1)|skin(1)	2	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
FGF14	2259	broad.mit.edu	37	13	102543276	102543276	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102543276delT	uc001vpe.2	-						FGF14_uc001vpf.2_Intron	NM_004115	NP_004106			fibroblast growth factor 14 isoform 1A						cell death|cell-cell signaling|JNK cascade|nervous system development|signal transduction	nucleus	growth factor activity|heparin binding			ovary(2)|lung(1)|large_intestine(1)	4	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	103128241	103128241	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103128241delA								FGF14 (74117 upstream) : TPP2 (121045 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	103644149	103644149	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103644149delA								LOC121952 (95766 upstream) : SLC10A2 (52201 downstream)																																			---	---	---	---
SLC10A2	6555	broad.mit.edu	37	13	103717882	103717882	+	Intron	DEL	C	-	-	rs61654237	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103717882delC	uc001vpy.3	-							NM_000452	NP_000443			solute carrier family 10 (sodium/bile acid						bile acid metabolic process|organic anion transport	integral to plasma membrane	bile acid:sodium symporter activity			ovary(3)|skin(1)	4	all_neural(89;0.0662)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	104500939	104500939	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:104500939delT								SLC10A2 (781743 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	105150286	105150289	+	IGR	DEL	CCTC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:105150286_105150289delCCTC								None (None upstream) : DAOA (967927 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	105303276	105303277	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:105303276_105303277insA								None (None upstream) : DAOA (814939 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	106476202	106476202	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106476202delC								DAOA (332820 upstream) : EFNB2 (665896 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	106866905	106866905	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106866905delT								DAOA (723523 upstream) : EFNB2 (275193 downstream)																																			---	---	---	---
ARGLU1	55082	broad.mit.edu	37	13	107196599	107196599	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107196599delA	uc001vqk.3	-							NM_018011	NP_060481			arginine and glutamate rich 1												0	Lung NSC(43;0.015)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	107758460	107758462	+	IGR	DEL	TTG	-	-	rs76956611		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107758460_107758462delTTG								ARGLU1 (537946 upstream) : FAM155A (62418 downstream)																																			---	---	---	---
FAM155A	728215	broad.mit.edu	37	13	107837752	107837753	+	Intron	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107837752_107837753delCT	uc001vql.2	-							NM_001080396	NP_001073865			family with sequence similarity 155, member A							integral to membrane	binding			skin(1)	1																		---	---	---	---
FAM155A	728215	broad.mit.edu	37	13	107910144	107910144	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107910144delG	uc001vql.2	-							NM_001080396	NP_001073865			family with sequence similarity 155, member A							integral to membrane	binding			skin(1)	1																		---	---	---	---
FAM155A	728215	broad.mit.edu	37	13	108440504	108440504	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108440504delT	uc001vql.2	-						uc001vqm.2_RNA	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	109842273	109842273	+	Intron	DEL	T	-	-	rs66894932		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109842273delT	uc001vqt.1	+						MYO16_uc010agk.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)															---	---	---	---
Unknown	0	broad.mit.edu	37	13	110492465	110492465	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110492465delT								IRS2 (53551 upstream) : COL4A1 (308846 downstream)																																			---	---	---	---
COL4A1	1282	broad.mit.edu	37	13	110861640	110861640	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110861640delT	uc001vqw.3	-						COL4A1_uc010agl.2_Intron	NM_001845	NP_001836			alpha 1 type IV collagen preproprotein						angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)															---	---	---	---
COL4A2	1284	broad.mit.edu	37	13	110991931	110991931	+	Intron	DEL	A	-	-	rs9521701	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110991931delA	uc001vqx.2	+							NM_001846	NP_001837			alpha 2 type IV collagen preproprotein						angiogenesis|axon guidance|extracellular matrix organization|negative regulation of angiogenesis	collagen type IV	extracellular matrix structural constituent|protein binding			skin(3)|central_nervous_system(2)|ovary(1)	6	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)															---	---	---	---
Unknown	0	broad.mit.edu	37	13	111410862	111410862	+	IGR	DEL	A	-	-	rs113710896		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111410862delA								ING1 (37442 upstream) : C13orf29 (105472 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	112220395	112220396	+	IGR	DEL	AT	-	-	rs67112505		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112220395_112220396delAT								C13orf16 (223802 upstream) : SOX1 (501517 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	112856642	112856642	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112856642delC								SOX1 (130622 upstream) : C13orf28 (174027 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	112918010	112918010	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112918010delA								SOX1 (191990 upstream) : C13orf28 (112659 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	114066502	114066502	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114066502delT								GRTP1 (48039 upstream) : ADPRHL1 (9758 downstream)																																			---	---	---	---
TFDP1	7027	broad.mit.edu	37	13	114267941	114267942	+	Intron	INS	-	GT	GT	rs149372254	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114267941_114267942insGT	uc001vtw.2	+						TFDP1_uc010tkd.1_Intron|TFDP1_uc010tke.1_Intron|TFDP1_uc001vty.3_Intron|TFDP1_uc010agx.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)			---	---	---	---
GAS6	2621	broad.mit.edu	37	13	114552474	114552475	+	Intron	DEL	AA	-	-	rs34045171		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114552474_114552475delAA	uc001vud.2	-							NM_000820	NP_000811			growth arrest-specific 6 isoform 1 precursor						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)																---	---	---	---
CDC16	8881	broad.mit.edu	37	13	115004335	115004335	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:115004335delT	uc001vuk.1	+						CDC16_uc010tkm.1_Intron|CDC16_uc001vul.1_Intron|CDC16_uc001vum.1_Intron|CDC16_uc001vun.1_Intron|CDC16_uc001vuo.1_Intron	NM_003903	NP_003894			anaphase-promoting complex, subunit 6						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|cell proliferation|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	binding				0	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)															---	---	---	---
Unknown	0	broad.mit.edu	37	14	19038307	19038308	+	IGR	INS	-	A	A	rs151060759		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19038307_19038308insA								None (None upstream) : OR11H12 (339286 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19047709	19047709	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19047709delA								None (None upstream) : OR11H12 (329885 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19106611	19106613	+	IGR	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19106611_19106613delAAA								None (None upstream) : OR11H12 (270981 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19120230	19120230	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19120230delT								None (None upstream) : OR11H12 (257364 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19339542	19339542	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19339542delA								None (None upstream) : OR11H12 (38052 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19462136	19462137	+	IGR	INS	-	A	A	rs111568347		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19462136_19462137insA								OR11H12 (83564 upstream) : POTEG (91228 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19506303	19506304	+	IGR	INS	-	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19506303_19506304insG								OR11H12 (127731 upstream) : POTEG (47061 downstream)																																			---	---	---	---
OR4Q3	441669	broad.mit.edu	37	14	20215067	20215068	+	5'Flank	INS	-	T	T	rs142988069	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20215067_20215068insT	uc010tkt.1	+							NM_172194	NP_751944			olfactory receptor, family 4, subfamily Q,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(3)	3	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	20727360	20727360	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20727360delT								OR11H4 (15436 upstream) : TTC5 (29943 downstream)																																			---	---	---	---
METT11D1	64745	broad.mit.edu	37	14	21460882	21460882	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21460882delT	uc001vyn.2	+						METT11D1_uc010tlk.1_3'UTR|METT11D1_uc001vym.2_Intron|METT11D1_uc001vyo.2_Intron|METT11D1_uc001vyp.2_Intron|METT11D1_uc001vyq.2_Intron	NM_022734	NP_073571			methyltransferase 11 domain containing 1 isoform						translation	mitochondrion|ribosome	copper ion binding|methyltransferase activity				0	all_cancers(95;0.00267)		OV - Ovarian serous cystadenocarcinoma(11;1.34e-10)|Epithelial(56;1.57e-08)|all cancers(55;7.45e-08)	GBM - Glioblastoma multiforme(265;0.0191)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	21643779	21643779	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21643779delA								OR5AU1 (19595 upstream) : HNRNPC (33519 downstream)																																			---	---	---	---
RPGRIP1	57096	broad.mit.edu	37	14	21756667	21756667	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21756667delT	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)														---	---	---	---
RPGRIP1	57096	broad.mit.edu	37	14	21776605	21776606	+	Intron	INS	-	C	C	rs72521765	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21776605_21776606insC	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22013336	22013337	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22013336_22013337delTT								SALL2 (7999 upstream) : OR10G3 (24598 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	22409532	22409540	+	Intron	DEL	TCTCTCTCT	-	-	rs3045130		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22409532_22409540delTCTCTCTCT	uc001wbw.2	+						uc010tmg.1_Intron|uc010tmh.1_Intron|uc010aiv.1_Intron|uc010tmi.1_Intron|uc010tmj.1_Intron|uc010aja.1_Intron|uc010ajb.1_Intron|uc001wck.2_Intron					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22981789	22981789	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22981789delA	uc001wbw.2	+						uc010aja.1_Intron|uc010tmk.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc001wcx.3_Intron|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|uc001wdv.3_Intron|uc001wec.2_Intron|uc001wee.3_Intron|uc010tmt.1_Intron|uc010ajv.1_Intron|uc001weg.2_Intron|uc001weh.1_Intron|uc001wei.2_Intron|uc001wej.2_Intron|uc001wek.2_Intron|uc001wel.2_Intron|uc001wem.3_Intron|uc001wen.1_Intron|uc001weo.2_Intron|uc001wep.2_Intron|uc001weq.2_Intron|uc001wer.2_Intron|uc001wet.2_Intron|uc001weu.2_Intron|uc001wev.2_Intron|uc001wew.2_Intron|uc010tmv.1_Intron|uc001wez.2_Intron|uc010ajx.1_Intron|uc001wfb.1_Intron|uc001wfd.1_Intron|uc001wfe.2_Intron|uc001wfg.2_Intron|uc001wfh.1_Intron|uc001wfi.2_5'Flank|uc001wfj.1_5'Flank|uc001wfk.2_5'Flank|uc001wfl.2_5'Flank|uc010ajy.1_5'Flank					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	23715801	23715801	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23715801delA								SLC7A8 (62952 upstream) : HOMEZ (27043 downstream)																																			---	---	---	---
THTPA	79178	broad.mit.edu	37	14	24010123	24010124	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24010123_24010124delTT	uc001wkb.3	+						uc001wkc.1_Intron|uc001wkf.1_Intron					Homo sapiens thiamine triphosphatase mRNA, complete cds.						dephosphorylation|generation of precursor metabolites and energy|thiamine metabolic process	cytosol|nucleolus|soluble fraction	thiamin-triphosphatase activity				0	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00643)	Thiamine(DB00152)													---	---	---	---
AP1G2	8906	broad.mit.edu	37	14	24034602	24034602	+	Intron	DEL	A	-	-	rs67953844		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24034602delA	uc001wkl.2	-						AP1G2_uc001wkj.2_Intron|AP1G2_uc001wkk.3_Intron|AP1G2_uc001wkn.2_Intron|uc001wko.1_Intron|AP1G2_uc001wkp.1_5'Flank|AP1G2_uc010tnp.1_Intron|AP1G2_uc010aks.2_3'UTR|AP1G2_uc010akt.2_3'UTR|AP1G2_uc010tnq.1_Intron	NM_003917	NP_003908			adaptor-related protein complex 1, gamma 2						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)														---	---	---	---
LRRC16B	90668	broad.mit.edu	37	14	24537638	24537638	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24537638delA	uc001wlj.2	+						LRRC16B_uc001wlk.2_Intron|CPNE6_uc010tnv.1_5'Flank|CPNE6_uc001wlm.2_5'Flank	NM_138360	NP_612369			leucine rich repeat containing 16B											ovary(2)|breast(2)|pancreas(1)	5				GBM - Glioblastoma multiforme(265;0.019)														---	---	---	---
TM9SF1	10548	broad.mit.edu	37	14	24673261	24673264	+	Intron	DEL	AAAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24673261_24673264delAAAA	uc010tob.1	-						TSSK4_uc001wne.2_5'Flank|TSSK4_uc001wnf.2_5'Flank|TSSK4_uc001wng.2_5'Flank|TSSK4_uc001wnh.2_5'Flank	NM_006405	NP_006396			transmembrane 9 superfamily member 1 isoform a						autophagy	autophagic vacuole membrane|cytoplasmic vesicle|integral to membrane|lysosomal membrane				ovary(1)	1				GBM - Glioblastoma multiforme(265;0.0183)														---	---	---	---
TGM1	7051	broad.mit.edu	37	14	24722653	24722654	+	Intron	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24722653_24722654delTG	uc001wod.2	-						TGM1_uc010tog.1_Intron	NM_000359	NP_000350			transglutaminase 1						cell envelope organization|keratinization|peptide cross-linking	cornified envelope|intrinsic to membrane	acyltransferase activity|metal ion binding|protein binding|protein-glutamine gamma-glutamyltransferase activity			central_nervous_system(2)|ovary(1)	3				GBM - Glioblastoma multiforme(265;0.0186)	L-Glutamine(DB00130)													---	---	---	---
Unknown	0	broad.mit.edu	37	14	25589037	25589037	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25589037delT								STXBP6 (69866 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	25624933	25624934	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25624933_25624934insA								STXBP6 (105762 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	26346681	26346681	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26346681delA								STXBP6 (827510 upstream) : NOVA1 (568409 downstream)																																			---	---	---	---
NOVA1	4857	broad.mit.edu	37	14	27049289	27049290	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:27049289_27049290insA	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	28397399	28397399	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:28397399delA								None (None upstream) : FOXG1 (838888 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	28557993	28557993	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:28557993delT								None (None upstream) : FOXG1 (678294 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	29185744	29185744	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29185744delC								None (None upstream) : FOXG1 (50543 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	29841164	29841165	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29841164_29841165delAC								C14orf23 (577165 upstream) : PRKD1 (204524 downstream)																																			---	---	---	---
PRKD1	5587	broad.mit.edu	37	14	30170193	30170196	+	Intron	DEL	CGCA	-	-	rs59057603	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30170193_30170196delCGCA	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)														---	---	---	---
HEATR5A	25938	broad.mit.edu	37	14	31885816	31885816	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31885816delA	uc010tpk.1	-						uc001wrh.2_Intron	NM_015473	NP_056288			HEAT repeat containing 5A								binding			ovary(1)	1	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)														---	---	---	---
AKAP6	9472	broad.mit.edu	37	14	33027070	33027070	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33027070delT	uc001wrq.2	+						AKAP6_uc010aml.2_Intron	NM_004274	NP_004265			A-kinase anchor protein 6						protein targeting	calcium channel complex|nuclear membrane|sarcoplasmic reticulum	protein kinase A binding|receptor binding			breast(6)|ovary(5)|lung(4)|skin(3)|large_intestine(2)|pancreas(1)	21	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)														---	---	---	---
NPAS3	64067	broad.mit.edu	37	14	33409027	33409027	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33409027delG	uc001wru.2	+						NPAS3_uc001wrs.2_Intron|NPAS3_uc001wrt.2_Intron|NPAS3_uc001wrv.2_Intron	NM_173159	NP_071406			neuronal PAS domain protein 3 isoform 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)|skin(1)	2	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)														---	---	---	---
NPAS3	64067	broad.mit.edu	37	14	33445067	33445072	+	Intron	DEL	GTGTGT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33445067_33445072delGTGTGT	uc001wru.2	+						NPAS3_uc001wrs.2_Intron|NPAS3_uc001wrt.2_Intron|NPAS3_uc001wrv.2_Intron	NM_173159	NP_071406			neuronal PAS domain protein 3 isoform 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)|skin(1)	2	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)														---	---	---	---
NPAS3	64067	broad.mit.edu	37	14	34054274	34054274	+	Intron	DEL	C	-	-	rs8014872	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34054274delC	uc001wru.2	+						NPAS3_uc001wrs.2_Intron|NPAS3_uc001wrt.2_Intron|NPAS3_uc001wrv.2_Intron|NPAS3_uc001wrw.2_Intron	NM_173159	NP_071406			neuronal PAS domain protein 3 isoform 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)|skin(1)	2	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	34554525	34554526	+	IGR	DEL	AA	-	-	rs79832433		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34554525_34554526delAA								EGLN3 (134238 upstream) : C14orf147 (347619 downstream)																																			---	---	---	---
BAZ1A	11177	broad.mit.edu	37	14	35238143	35238143	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35238143delA	uc001wsk.2	-						BAZ1A_uc001wsl.2_Intron	NM_013448	NP_038476			bromodomain adjacent to zinc finger domain, 1A						chromatin remodeling|regulation of transcription, DNA-dependent|transcription, DNA-dependent	ACF complex	zinc ion binding			lung(2)|central_nervous_system(2)|ovary(1)|breast(1)|skin(1)	7	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)														---	---	---	---
SRP54	6729	broad.mit.edu	37	14	35495604	35495604	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35495604delT	uc001wso.2	+						SRP54_uc010tpp.1_Intron|SRP54_uc010tpq.1_Intron	NM_003136	NP_003127			signal recognition particle 54kDa isoform 1						GTP catabolic process|response to drug|SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition|SRP-dependent cotranslational protein targeting to membrane, translocation	cytosol|nuclear speck|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding|drug binding|endoplasmic reticulum signal peptide binding|GDP binding|GTP binding|nucleoside-triphosphatase activity|ribonucleoprotein binding			ovary(1)	1	Breast(36;0.0545)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;2.48e-05)|Lung(238;3.13e-05)|Epithelial(34;0.0314)|all cancers(34;0.0797)|BRCA - Breast invasive adenocarcinoma(188;0.243)	GBM - Glioblastoma multiforme(112;0.0396)														---	---	---	---
KIAA0391	9692	broad.mit.edu	37	14	35610425	35610425	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35610425delT	uc001wsy.1	+						KIAA0391_uc010tps.1_Intron|KIAA0391_uc001wsz.1_Intron|KIAA0391_uc001wta.2_Intron|KIAA0391_uc001wtb.1_Intron|KIAA0391_uc001wtc.1_Intron	NM_014672	NP_055487			mitochondrial RNase P protein 3 precursor						tRNA processing	mitochondrion					0	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;2.93e-05)|LUAD - Lung adenocarcinoma(48;3.86e-05)|Epithelial(34;0.0114)|all cancers(34;0.0277)	GBM - Glioblastoma multiforme(112;0.0593)														---	---	---	---
PSMA6	5687	broad.mit.edu	37	14	35767704	35767704	+	Intron	DEL	A	-	-	rs75036330		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35767704delA	uc001wtd.2	+						KIAA0391_uc001wta.2_Intron|PSMA6_uc010tpt.1_Intron|PSMA6_uc010tpu.1_Intron	NM_002791	NP_002782			proteasome alpha 6 subunit						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of NF-kappaB transcription factor activity|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	mitochondrion|nuclear matrix|polysome|proteasome core complex, alpha-subunit complex|sarcomere	NF-kappaB binding|purine ribonucleoside triphosphate binding|RNA binding|threonine-type endopeptidase activity				0	Breast(36;0.0519)|Hepatocellular(127;0.158)		Lung(238;3.81e-05)|LUAD - Lung adenocarcinoma(48;5.59e-05)|Epithelial(34;0.00342)|all cancers(34;0.00973)	GBM - Glioblastoma multiforme(112;0.0234)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	36643191	36643191	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36643191delT								BRMS1L (302023 upstream) : MBIP (124573 downstream)																																			---	---	---	---
MBIP	51562	broad.mit.edu	37	14	36770037	36770038	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36770037_36770038delAA	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)														---	---	---	---
SLC25A21	89874	broad.mit.edu	37	14	37612795	37612798	+	Intron	DEL	GTGT	-	-	rs146683942		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37612795_37612798delGTGT	uc001wtz.1	-							NM_030631	NP_085134			solute carrier family 25 (mitochondrial						lysine catabolic process	integral to membrane|mitochondrial inner membrane	alpha-ketoglutarate transmembrane transporter activity|binding			skin(1)	1	Esophageal squamous(585;0.164)|Breast(36;0.179)|Hepatocellular(127;0.213)		Lung(8;2.16e-08)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.0112)|all cancers(34;0.0274)|LUSC - Lung squamous cell carcinoma(13;0.149)	GBM - Glioblastoma multiforme(112;0.00204)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	38097001	38097002	+	Intron	INS	-	G	G	rs111914382		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38097001_38097002insG	uc001wug.2	+											Homo sapiens chromosome 14 open reading frame 25, mRNA (cDNA clone IMAGE:5268731), partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	39023375	39023376	+	IGR	INS	-	TCCT	TCCT	rs147304995	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39023375_39023376insTCCT								CLEC14A (297801 upstream) : SEC23A (477747 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	39915972	39915973	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39915972_39915973delTC								FBXO33 (14268 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	40532615	40532616	+	IGR	DEL	TG	-	-	rs56331630	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:40532615_40532616delTG								FBXO33 (630911 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	41250911	41250912	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:41250911_41250912delTT								None (None upstream) : LRFN5 (825852 downstream)																																			---	---	---	---
LRFN5	145581	broad.mit.edu	37	14	42138499	42138500	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42138499_42138500insA	uc001wvm.2	+							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)			---	---	---	---
LRFN5	145581	broad.mit.edu	37	14	42208861	42208861	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42208861delA	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	42544438	42544438	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42544438delA								LRFN5 (170688 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	42557073	42557074	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42557073_42557074delTG								LRFN5 (183323 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	43978703	43978703	+	IGR	DEL	G	-	-	rs78308216		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:43978703delG								None (None upstream) : FSCB (994652 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44433391	44433391	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44433391delA								None (None upstream) : FSCB (539964 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44564926	44564926	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44564926delC								None (None upstream) : FSCB (408429 downstream)																																			---	---	---	---
KLHL28	54813	broad.mit.edu	37	14	45400413	45400415	+	Intron	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45400413_45400415delTTT	uc001wvq.2	-						KLHL28_uc001wvr.2_Intron	NM_017658	NP_060128			BTB (POZ) domain containing 5											ovary(1)	1																		---	---	---	---
FAM179B	23116	broad.mit.edu	37	14	45540826	45540826	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45540826delT	uc001wvv.2	+						FAM179B_uc001wvw.2_Intron|FAM179B_uc010anc.2_Intron	NM_015091	NP_055906			hypothetical protein LOC23116								binding			skin(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	46014107	46014108	+	IGR	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:46014107_46014108delCT								C14orf106 (291502 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	46554699	46554699	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:46554699delT								C14orf106 (832094 upstream) : RPL10L (565523 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	46618442	46618446	+	IGR	DEL	TTTGT	-	-	rs139706144		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:46618442_46618446delTTTGT								C14orf106 (895837 upstream) : RPL10L (501776 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	49426342	49426343	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:49426342_49426343delAA								None (None upstream) : SDCCAG1 (606684 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	49980411	49980411	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:49980411delA								None (None upstream) : SDCCAG1 (52616 downstream)																																			---	---	---	---
SDCCAG1	9147	broad.mit.edu	37	14	50047909	50047909	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50047909delA	uc010anj.1	-						RPS29_uc001wwl.2_Intron	NM_004713	NP_004704			serologically defined colon cancer antigen 1							cytoplasm|nucleus					0	all_epithelial(31;0.000822)|Breast(41;0.0117)	all_lung(585;1.02e-05)		OV - Ovarian serous cystadenocarcinoma(311;5.99e-34)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	50350120	50350121	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50350120_50350121insA								SDCCAG1 (30581 upstream) : ARF6 (9615 downstream)																																			---	---	---	---
MAP4K5	11183	broad.mit.edu	37	14	50894989	50894990	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50894989_50894990delTT	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)																	---	---	---	---
MAP4K5	11183	broad.mit.edu	37	14	50952368	50952368	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50952368delA	uc001wya.2	-						MAP4K5_uc001wyb.2_Intron|MAP4K5_uc010anv.1_Intron	NM_006575	NP_006566			mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			large_intestine(1)	1	all_epithelial(31;0.000415)|Breast(41;0.0102)																	---	---	---	---
MAP4K5	11183	broad.mit.edu	37	14	50959760	50959760	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50959760delA	uc001wya.2	-						MAP4K5_uc001wyb.2_Intron|MAP4K5_uc010anv.1_Intron	NM_006575	NP_006566			mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			large_intestine(1)	1	all_epithelial(31;0.000415)|Breast(41;0.0102)																	---	---	---	---
Unknown	0	broad.mit.edu	37	14	51161876	51161876	+	IGR	DEL	A	-	-	rs77011075		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51161876delA								SAV1 (26853 upstream) : NIN (24606 downstream)																																			---	---	---	---
NIN	51199	broad.mit.edu	37	14	51258530	51258531	+	Intron	INS	-	ACAA	ACAA			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51258530_51258531insACAA	uc001wym.2	-						NIN_uc001wyi.2_Intron|NIN_uc001wyj.2_Intron|NIN_uc001wyk.2_Intron|NIN_uc010tqp.1_Intron|NIN_uc001wyo.2_Intron|NIN_uc001wyp.1_Intron	NM_182946	NP_891991			ninein isoform 5						centrosome localization	centrosome|microtubule	calcium ion binding|GTP binding|protein binding			skin(3)|ovary(1)|kidney(1)|central_nervous_system(1)	6	all_epithelial(31;0.00244)|Breast(41;0.127)							T	PDGFRB	MPD								---	---	---	---
ABHD12B	145447	broad.mit.edu	37	14	51348148	51348148	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51348148delT	uc001wys.2	+						ABHD12B_uc001wyq.2_Intron|ABHD12B_uc001wyr.2_Intron|ABHD12B_uc010any.2_Intron	NM_181533	NP_853511			abhydrolase domain containing 12B isoform b								hydrolase activity			breast(1)	1	all_epithelial(31;0.00481)|Breast(41;0.148)																	---	---	---	---
Unknown	0	broad.mit.edu	37	14	51733526	51733526	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51733526delT								TMX1 (9156 upstream) : FRMD6 (222329 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	51859774	51859774	+	IGR	DEL	A	-	-	rs74786368		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51859774delA								TMX1 (135404 upstream) : FRMD6 (96081 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	51872293	51872293	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51872293delT								TMX1 (147923 upstream) : FRMD6 (83562 downstream)																																			---	---	---	---
GNG2	54331	broad.mit.edu	37	14	52320606	52320606	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52320606delT	uc001wzh.2	+											Homo sapiens guanine nucleotide binding protein gamma 2 (GNG2) mRNA, complete cds.						cellular response to glucagon stimulus|energy reserve metabolic process|platelet activation|synaptic transmission	heterotrimeric G-protein complex	protein binding|signal transducer activity				0	all_epithelial(31;0.0659)|Breast(41;0.0684)				Halothane(DB01159)													---	---	---	---
Unknown	0	broad.mit.edu	37	14	52610995	52610995	+	IGR	DEL	T	-	-	rs11300019		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52610995delT								NID2 (75049 upstream) : PTGDR (123436 downstream)																																			---	---	---	---
STYX	6815	broad.mit.edu	37	14	53235544	53235545	+	Intron	DEL	TA	-	-	rs2274274	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53235544_53235545delTA	uc010tqy.1	+						STYX_uc001xaa.2_Intron	NM_001130701	NP_001124173			serine/threonine/tyrosine interacting protein						protein dephosphorylation|spermatogenesis	cytoplasm	protein tyrosine/serine/threonine phosphatase activity				0	Breast(41;0.176)																	---	---	---	---
Unknown	0	broad.mit.edu	37	14	53802502	53802502	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53802502delG								DDHD1 (182456 upstream) : BMP4 (613955 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	53989937	53989938	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53989937_53989938delAA								DDHD1 (369891 upstream) : BMP4 (426519 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	54961262	54961262	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54961262delT								GMFB (5518 upstream) : CGRRF1 (15325 downstream)																																			---	---	---	---
SAMD4A	23034	broad.mit.edu	37	14	55231287	55231287	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55231287delT	uc001xbb.2	+						SAMD4A_uc001xbc.2_Intron|SAMD4A_uc001xbg.2_Intron	NM_015589	NP_056404			sterile alpha motif domain containing 4 isoform						positive regulation of translation	cell junction|cytoplasm|dendrite|synapse|synaptosome	translation repressor activity				0																		---	---	---	---
SAMD4A	23034	broad.mit.edu	37	14	55257391	55257392	+	3'UTR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55257391_55257392delTG	uc001xbb.2	+	12					SAMD4A_uc001xbc.2_3'UTR|SAMD4A_uc001xbg.2_3'UTR	NM_015589	NP_056404			sterile alpha motif domain containing 4 isoform						positive regulation of translation	cell junction|cytoplasm|dendrite|synapse|synaptosome	translation repressor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	55280066	55280066	+	IGR	DEL	G	-	-	rs59837412		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55280066delG								SAMD4A (20033 upstream) : GCH1 (28658 downstream)																																			---	---	---	---
GCH1	2643	broad.mit.edu	37	14	55366587	55366587	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55366587delT	uc001xbh.1	-						GCH1_uc001xbi.1_Intron|GCH1_uc001xbj.1_Intron|GCH1_uc001xbk.1_Intron|GCH1_uc010aol.1_Intron|GCH1_uc001xbl.1_Intron	NM_001024024	NP_001019195			GTP cyclohydrolase 1 isoform 1						dopamine biosynthetic process|GTP catabolic process|neuromuscular process controlling posture|nitric oxide biosynthetic process|positive regulation of nitric-oxide synthase activity|protein homooligomerization|response to interferon-gamma|response to lipopolysaccharide|response to pain|response to tumor necrosis factor|tetrahydrobiopterin biosynthetic process|tetrahydrofolate biosynthetic process	cytoplasmic vesicle|cytosol|nuclear membrane|protein complex	GTP binding|GTP cyclohydrolase I activity|protein homodimerization activity|zinc ion binding			skin(1)	1																		---	---	---	---
KIAA0831	22863	broad.mit.edu	37	14	55876280	55876280	+	Intron	DEL	A	-	-	rs35648229		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55876280delA	uc001xbx.1	-						FBXO34_uc001xbv.2_Intron	NM_014924	NP_055739			Barkor						autophagic vacuole assembly|positive regulation of autophagy	autophagic vacuole|endoplasmic reticulum|pre-autophagosomal structure membrane	protein binding				0																		---	---	---	---
KTN1	3895	broad.mit.edu	37	14	56150981	56150981	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56150981delA	uc001xcb.2	+	46					KTN1_uc001xce.2_3'UTR|KTN1_uc001xcc.2_3'UTR|KTN1_uc001xcd.2_3'UTR|KTN1_uc010trb.1_3'UTR|KTN1_uc010aoq.2_3'UTR|KTN1_uc010trc.1_3'UTR|KTN1_uc001xcg.2_3'UTR	NM_182926	NP_891556			kinectin 1 isoform a						microtubule-based movement	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction				breast(3)|ovary(2)|lung(1)|central_nervous_system(1)	7								T	RET	papillary thryoid								---	---	---	---
Unknown	0	broad.mit.edu	37	14	56446836	56446836	+	IGR	DEL	T	-	-	rs35595895		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56446836delT								C14orf34 (183444 upstream) : PELI2 (138257 downstream)																																			---	---	---	---
C14orf101	54916	broad.mit.edu	37	14	57055273	57055273	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57055273delT	uc001xcm.2	+						C14orf101_uc001xcj.2_Intron|C14orf101_uc001xck.2_Intron|C14orf101_uc010aot.1_Intron|C14orf101_uc001xcl.1_Intron|C14orf101_uc001xcn.2_Intron|C14orf101_uc010trf.1_Intron	NM_017799	NP_060269			hypothetical protein LOC54916							integral to membrane				breast(1)|central_nervous_system(1)	2				OV - Ovarian serous cystadenocarcinoma(311;0.226)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	57376034	57376034	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57376034delT	uc001xcr.1	+											Homo sapiens cDNA clone IMAGE:5492202, partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	57494539	57494539	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57494539delT								OTX2 (217355 upstream) : EXOC5 (174657 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	58250965	58250966	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58250965_58250966insA								SLC35F4 (187350 upstream) : C14orf37 (219843 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	58424603	58424604	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58424603_58424604delAC								SLC35F4 (360988 upstream) : C14orf37 (46205 downstream)																																			---	---	---	---
C14orf37	145407	broad.mit.edu	37	14	58604646	58604646	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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	58690726	58690726	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58690726delT	uc010tro.1	-						ACTR10_uc001xdf.2_Intron|ACTR10_uc001xdg.2_Intron|ACTR10_uc001xdh.2_Intron|ACTR10_uc010trp.1_Intron|ACTR10_uc010apc.2_Intron	NM_001001872	NP_001001872			hypothetical protein LOC145407 precursor							integral to membrane	binding				0																		---	---	---	---
DACT1	51339	broad.mit.edu	37	14	59101987	59101988	+	5'Flank	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59101987_59101988delAA	uc001xdw.2	+						DACT1_uc010trv.1_Intron|DACT1_uc001xdx.2_5'Flank	NM_016651	NP_057735			dapper 1 isoform 1						multicellular organismal development|Wnt receptor signaling pathway	cytoplasm|nucleus				large_intestine(2)|lung(2)|ovary(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	59195221	59195224	+	IGR	DEL	GTGT	-	-	rs72039933		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59195221_59195224delGTGT								DACT1 (80185 upstream) : DAAM1 (460175 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	59613921	59613921	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59613921delA								DACT1 (498885 upstream) : DAAM1 (41478 downstream)																																			---	---	---	---
RTN1	6252	broad.mit.edu	37	14	60096966	60096966	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60096966delA	uc001xen.1	-						RTN1_uc001xem.1_Intron|RTN1_uc001xek.1_Intron|RTN1_uc001xel.1_Intron|RTN1_uc010apl.1_Intron	NM_021136	NP_066959			reticulon 1 isoform A						neuron differentiation	integral to endoplasmic reticulum membrane	signal transducer activity			ovary(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0968)														---	---	---	---
RTN1	6252	broad.mit.edu	37	14	60258571	60258571	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60258571delT	uc001xen.1	-							NM_021136	NP_066959			reticulon 1 isoform A						neuron differentiation	integral to endoplasmic reticulum membrane	signal transducer activity			ovary(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0968)														---	---	---	---
C14orf135	64430	broad.mit.edu	37	14	60603242	60603242	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60603242delT	uc001xeq.2	+							NM_022495	NP_071940			hepatitis C virus F protein-binding protein 2							integral to membrane				ovary(2)	2		Myeloproliferative disorder(585;0.163)		OV - Ovarian serous cystadenocarcinoma(108;0.127)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	60671336	60671336	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60671336delA								DHRS7 (34775 upstream) : PPM1A (41134 downstream)																																			---	---	---	---
SLC38A6	145389	broad.mit.edu	37	14	61518736	61518736	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61518736delT	uc001xfg.1	+						SLC38A6_uc001xfh.1_Intron|SLC38A6_uc001xfi.2_Intron|SLC38A6_uc001xfj.1_Intron|SLC38A6_uc001xfk.2_Intron|SLC38A6_uc010trz.1_Intron	NM_153811	NP_722518			solute carrier family 38, member 6						amino acid transport|sodium ion transport	integral to membrane				ovary(1)|central_nervous_system(1)|skin(1)	3				OV - Ovarian serous cystadenocarcinoma(108;0.0981)														---	---	---	---
SLC38A6	145389	broad.mit.edu	37	14	61533233	61533233	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61533233delA	uc001xfh.1	+						SLC38A6_uc001xfi.2_Intron|SLC38A6_uc001xfk.2_Intron|SLC38A6_uc010trz.1_Intron	NM_153811	NP_722518			solute carrier family 38, member 6						amino acid transport|sodium ion transport	integral to membrane				ovary(1)|central_nervous_system(1)|skin(1)	3				OV - Ovarian serous cystadenocarcinoma(108;0.0981)														---	---	---	---
SNAPC1	6617	broad.mit.edu	37	14	62260287	62260287	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62260287delT	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	62267413	62267413	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62267413delA								SNAPC1 (4268 upstream) : SYT16 (186390 downstream)																																			---	---	---	---
KCNH5	27133	broad.mit.edu	37	14	63247727	63247728	+	Intron	DEL	AA	-	-	rs76725095		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63247727_63247728delAA	uc001xfx.2	-						KCNH5_uc001xfy.2_Intron|KCNH5_uc001xfz.1_Intron	NM_139318	NP_647479			potassium voltage-gated channel, subfamily H,						regulation of transcription, DNA-dependent	integral to membrane	calmodulin binding|two-component sensor activity|voltage-gated potassium channel activity			ovary(4)|skin(4)|central_nervous_system(1)	9				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)														---	---	---	---
KCNH5	27133	broad.mit.edu	37	14	63529443	63529443	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63529443delC	uc001xfz.1	-						KCNH5_uc001xga.2_Intron	NM_172376	NP_758964			potassium voltage-gated channel, subfamily H,						regulation of transcription, DNA-dependent	integral to membrane	calmodulin binding|two-component sensor activity|voltage-gated potassium channel activity			ovary(4)|skin(4)|central_nervous_system(1)	9				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)														---	---	---	---
PPP2R5E	5529	broad.mit.edu	37	14	63853642	63853643	+	Intron	DEL	AA	-	-	rs76815717		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63853642_63853643delAA	uc001xgd.1	-						PPP2R5E_uc010tsf.1_Intron|PPP2R5E_uc010tsg.1_Intron|PPP2R5E_uc001xge.2_Intron|PPP2R5E_uc010tsh.1_Intron|PPP2R5E_uc001xgf.1_Intron	NM_006246	NP_006237			epsilon isoform of regulatory subunit B56,						signal transduction	cytoplasm|intracellular membrane-bounded organelle|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.00197)|all cancers(60;0.0153)|BRCA - Breast invasive adenocarcinoma(234;0.128)														---	---	---	---
PPP2R5E	5529	broad.mit.edu	37	14	63964485	63964486	+	Intron	INS	-	A	A	rs151045786	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63964485_63964486insA	uc001xgd.1	-						PPP2R5E_uc010tsf.1_Intron|PPP2R5E_uc010tsg.1_Intron|PPP2R5E_uc001xge.2_Intron|PPP2R5E_uc010tsh.1_Intron|PPP2R5E_uc001xgf.1_Intron|PPP2R5E_uc001xgg.3_Intron	NM_006246	NP_006237			epsilon isoform of regulatory subunit B56,						signal transduction	cytoplasm|intracellular membrane-bounded organelle|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.00197)|all cancers(60;0.0153)|BRCA - Breast invasive adenocarcinoma(234;0.128)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	64017350	64017350	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64017350delA								PPP2R5E (7271 upstream) : WDR89 (46408 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	64114497	64114497	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64114497delA								WDR89 (5906 upstream) : SGPP1 (36440 downstream)																																			---	---	---	---
SGPP1	81537	broad.mit.edu	37	14	64181549	64181549	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64181549delT	uc001xgj.2	-							NM_030791	NP_110418			sphingosine-1-phosphate phosphatase 1							endoplasmic reticulum membrane|integral to membrane	dihydrosphingosine-1-phosphate phosphatase activity|sphingosine-1-phosphate phosphatase activity			central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.0056)|all cancers(60;0.0141)|BRCA - Breast invasive adenocarcinoma(234;0.103)														---	---	---	---
MTHFD1	4522	broad.mit.edu	37	14	64867679	64867679	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64867679delT	uc001xhb.2	+						MTHFD1_uc010aqe.2_Intron|MTHFD1_uc010aqf.2_Intron	NM_005956	NP_005947			methylenetetrahydrofolate dehydrogenase 1						folic acid metabolic process|folic acid-containing compound biosynthetic process|histidine biosynthetic process|methionine biosynthetic process|one-carbon metabolic process|purine nucleotide biosynthetic process	cytosol|mitochondrion	ATP binding|formate-tetrahydrofolate ligase activity|methenyltetrahydrofolate cyclohydrolase activity|methylenetetrahydrofolate dehydrogenase (NADP+) activity|methylenetetrahydrofolate dehydrogenase|protein binding			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(108;8.7e-12)|all cancers(60;3.29e-11)|BRCA - Breast invasive adenocarcinoma(234;0.0488)	NADH(DB00157)|Tetrahydrofolic acid(DB00116)													---	---	---	---
FNTB	2342	broad.mit.edu	37	14	65453494	65453494	+	5'Flank	DEL	G	-	-	rs3215788		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65453494delG	uc001xia.2	+						FNTB_uc010tsl.1_Intron|FNTB_uc010tsm.1_Intron|uc001xib.2_5'Flank	NM_002028	NP_002019			farnesyltransferase, CAAX box, beta						protein farnesylation	microtubule associated complex	protein binding|protein farnesyltransferase activity			ovary(1)	1				all cancers(60;0.00115)|OV - Ovarian serous cystadenocarcinoma(108;0.00412)|BRCA - Breast invasive adenocarcinoma(234;0.011)												OREG0022738	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	65604485	65604485	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65604485delG								MAX (35258 upstream) : LOC645431 (272828 downstream)																																			---	---	---	---
GPHN	10243	broad.mit.edu	37	14	67599344	67599344	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67599344delT	uc001xiy.2	+						GPHN_uc001xix.2_Intron|GPHN_uc010tss.1_Intron|GPHN_uc010tst.1_Intron|GPHN_uc010tsu.1_Intron	NM_001024218	NP_001019389			gephyrin isoform 2						Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cell junction|cytoplasm|cytoskeleton|postsynaptic membrane	ATP binding|metal ion binding|nucleotidyltransferase activity			ovary(2)	2		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)				T	MLL	AL								---	---	---	---
ZFYVE26	23503	broad.mit.edu	37	14	68244576	68244577	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68244576_68244577delTT	uc001xka.2	-						ZFYVE26_uc010tsz.1_Intron|ZFYVE26_uc001xkc.3_Intron	NM_015346	NP_056161			zinc finger, FYVE domain containing 26						cell cycle|cell death|cytokinesis|double-strand break repair via homologous recombination	centrosome|midbody	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			ovary(9)|breast(2)	11				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)														---	---	---	---
RAD51L1	5890	broad.mit.edu	37	14	68756431	68756432	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68756431_68756432delAA	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	69649380	69649381	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69649380_69649381delTC								DCAF5 (29466 upstream) : EXD2 (8865 downstream)																																			---	---	---	---
SLC39A9	55334	broad.mit.edu	37	14	69919256	69919256	+	Intron	DEL	A	-	-	rs11286169		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69919256delA	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)														---	---	---	---
SFRS5	6430	broad.mit.edu	37	14	70237110	70237110	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70237110delT	uc001xll.2	+						SFRS5_uc001xlm.2_RNA|SFRS5_uc001xln.1_3'UTR|SFRS5_uc001xlo.2_Intron|SFRS5_uc001xlp.2_Intron|SFRS5_uc001xlq.2_Intron	NM_006925	NP_008856			splicing factor, arginine/serine-rich 5						mRNA 3'-end processing|mRNA export from nucleus|mRNA splice site selection|termination of RNA polymerase II transcription	nuclear speck	nucleotide binding|protein binding|RNA binding				0				all cancers(60;0.00144)|BRCA - Breast invasive adenocarcinoma(234;0.0132)|OV - Ovarian serous cystadenocarcinoma(108;0.0154)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	70284369	70284370	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70284369_70284370delAC								SLC10A1 (20363 upstream) : SMOC1 (61773 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	70773729	70773729	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70773729delT								ADAM21P1 (59211 upstream) : COX16 (18070 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	70888801	70888801	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70888801delT								SYNJ2BP (4994 upstream) : ADAM21 (35416 downstream)																																			---	---	---	---
ADAM21	8747	broad.mit.edu	37	14	70926260	70926261	+	Frame_Shift_Ins	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70926260_70926261insT	uc001xmd.2	+	1	2044_2045	c.2044_2045insT	c.(2044-2046)GTTfs	p.V682fs		NM_003813	NP_003804	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21 preproprotein	682	Helical; (Potential).				proteolysis|single fertilization	integral to membrane	metalloendopeptidase activity|zinc ion binding			pancreas(1)|skin(1)	2				all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)														---	---	---	---
SIPA1L1	26037	broad.mit.edu	37	14	71995830	71995831	+	5'Flank	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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	72463262	72463262	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72463262delG	uc001xna.3	+						RGS6_uc010ttn.1_Intron|RGS6_uc001xmx.3_Intron|RGS6_uc010tto.1_Intron|RGS6_uc001xmy.3_Intron	NM_004296	NP_004287			regulator of G-protein signalling 6						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			upper_aerodigestive_tract(1)|lung(1)|skin(1)	3				all cancers(60;0.00309)|BRCA - Breast invasive adenocarcinoma(234;0.0281)|STAD - Stomach adenocarcinoma(64;0.0302)|OV - Ovarian serous cystadenocarcinoma(108;0.0476)														---	---	---	---
DPF3	8110	broad.mit.edu	37	14	73133838	73133838	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73133838delT	uc001xnc.2	-						DPF3_uc001xnd.1_Intron|DPF3_uc001xnf.2_Intron	NM_012074	NP_036206			D4, zinc and double PHD fingers, family 3						chromatin modification|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nBAF complex	nucleic acid binding|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00649)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)														---	---	---	---
DPF3	8110	broad.mit.edu	37	14	73300277	73300277	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73300277delA	uc001xnc.2	-						DPF3_uc001xnf.2_Intron|DPF3_uc010ari.1_Intron|DPF3_uc010ttq.1_Intron	NM_012074	NP_036206			D4, zinc and double PHD fingers, family 3						chromatin modification|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nBAF complex	nucleic acid binding|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00649)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	74270311	74270311	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74270311delA								C14orf43 (16415 upstream) : PTGR2 (48223 downstream)																																			---	---	---	---
ZNF410	57862	broad.mit.edu	37	14	74363668	74363668	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74363668delA	uc001xoz.1	+						ZNF410_uc001xoy.1_Intron|ZNF410_uc010ary.1_Intron|ZNF410_uc010tuf.1_Intron|ZNF410_uc010tug.1_Intron|ZNF410_uc010tuh.1_Intron|ZNF410_uc010tui.1_Intron|ZNF410_uc010arz.1_Intron|ZNF410_uc001xpa.1_Intron|ZNF410_uc001xpb.1_Intron|ZNF410_uc001xpc.1_Intron|ZNF410_uc010tuj.1_5'Flank	NM_021188	NP_067011			zinc finger protein 410						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00369)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	74779458	74779462	+	IGR	DEL	TTTTT	-	-	rs151066195		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74779458_74779462delTTTTT								ABCD4 (9691 upstream) : C14orf115 (35704 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	75405636	75405637	+	IGR	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75405636_75405637delCT								RPS6KL1 (15678 upstream) : PGF (2903 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	75729263	75729263	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75729263delA								TMED10 (85914 upstream) : FOS (16218 downstream)																																			---	---	---	---
TTLL5	23093	broad.mit.edu	37	14	76185973	76185973	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76185973delA	uc001xrx.2	+						TTLL5_uc010ask.1_Intron|TTLL5_uc001xry.1_Intron	NM_015072	NP_055887			tubulin tyrosine ligase-like family, member 5						protein modification process|transcription, DNA-dependent	centrosome|cilium|microtubule basal body|nucleus	tubulin-tyrosine ligase activity			ovary(2)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.029)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	76592591	76592591	+	IGR	DEL	A	-	-	rs35107231		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76592591delA								C14orf179 (41661 upstream) : C14orf118 (25668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	77252509	77252510	+	RNA	DEL	TC	-	-	rs1989376		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77252509_77252510delTC	uc001xsu.1	-	1		c.558_559delGA								Homo sapiens cDNA FLJ43739 fis, clone TESTI2015375.																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	77345019	77345019	+	IGR	DEL	T	-	-	rs77002581		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77345019delT								C14orf166B (8374 upstream) : C14orf4 (145869 downstream)																																			---	---	---	---
SPTLC2	9517	broad.mit.edu	37	14	77974370	77974370	+	3'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77974370delT	uc001xub.2	-	12						NM_004863	NP_004854			serine palmitoyltransferase, long chain base							integral to membrane|serine C-palmitoyltransferase complex	pyridoxal phosphate binding|serine C-palmitoyltransferase activity|transferase activity, transferring nitrogenous groups			upper_aerodigestive_tract(1)|ovary(1)	2			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0346)	L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)													---	---	---	---
ADCK1	57143	broad.mit.edu	37	14	78298325	78298326	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78298325_78298326delTT	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	78655929	78655929	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78655929delT	uc001xum.1	+											Homo sapiens mRNA for KIAA0743 protein, partial cds.						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)														---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	79018188	79018188	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79018188delT	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	79175467	79175467	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79175467delT	uc001xun.2	+						NRXN3_uc001xum.1_Intron|NRXN3_uc010asv.1_Intron	NM_004796	NP_004787			neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)														---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	79347750	79347750	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79347750delT	uc001xun.2	+						NRXN3_uc001xum.1_Intron|NRXN3_uc010asv.1_Intron	NM_004796	NP_004787			neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)														---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	79394648	79394648	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79394648delT	uc001xun.2	+						NRXN3_uc001xum.1_Intron|NRXN3_uc010asv.1_Intron	NM_004796	NP_004787			neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)														---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	80025997	80025997	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80025997delA	uc001xun.2	+						NRXN3_uc001xum.1_Intron|NRXN3_uc001xup.2_Intron|NRXN3_uc001xuq.2_Intron|NRXN3_uc010asw.2_Intron|NRXN3_uc001xur.3_Intron	NM_004796	NP_004787			neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)														---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	80050156	80050156	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80050156delC	uc001xun.2	+						NRXN3_uc001xum.1_Intron|NRXN3_uc001xup.2_Intron|NRXN3_uc001xuq.2_Intron|NRXN3_uc010asw.2_Intron|NRXN3_uc001xur.3_Intron	NM_004796	NP_004787			neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)														---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	80152586	80152586	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80152586delA	uc001xun.2	+						NRXN3_uc001xum.1_Intron|NRXN3_uc001xup.2_Intron|NRXN3_uc001xuq.2_Intron|NRXN3_uc010asw.2_Intron|NRXN3_uc001xur.3_Intron	NM_004796	NP_004787			neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)														---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	80172345	80172346	+	Intron	INS	-	TA	TA	rs138996568	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80172345_80172346insTA	uc001xun.2	+						NRXN3_uc001xum.1_Intron|NRXN3_uc001xup.2_Intron|NRXN3_uc001xuq.2_Intron|NRXN3_uc010asw.2_Intron|NRXN3_uc001xur.3_Intron	NM_004796	NP_004787			neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)														---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	80204074	80204074	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80204074delT	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)														---	---	---	---
TSHR	7253	broad.mit.edu	37	14	81557384	81557384	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81557384delT	uc001xvd.1	+						TSHR_uc001xvb.1_Intron|TSHR_uc001xvc.2_Intron|TSHR_uc010tvs.1_Intron	NM_000369	NP_000360			thyroid stimulating hormone receptor isoform 1						cell-cell signaling|positive regulation of cell proliferation	integral to plasma membrane	protein binding|thyroid-stimulating hormone receptor activity			thyroid(289)|ovary(5)|lung(3)|kidney(1)|skin(1)	299				BRCA - Breast invasive adenocarcinoma(234;0.0402)	Thyrotropin Alfa(DB00024)			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism 						---	---	---	---
STON2	85439	broad.mit.edu	37	14	81746049	81746049	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81746049delA	uc010tvu.1	-						STON2_uc001xvk.1_Intron|STON2_uc010tvt.1_5'Flank	NM_033104	NP_149095			stonin 2						endocytosis|intracellular protein transport|regulation of endocytosis	clathrin adaptor complex|nucleolus	protein binding			skin(3)|pancreas(2)	5				BRCA - Breast invasive adenocarcinoma(234;0.0348)														---	---	---	---
STON2	85439	broad.mit.edu	37	14	81804010	81804010	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81804010delA	uc010tvu.1	-						STON2_uc001xvk.1_Intron	NM_033104	NP_149095			stonin 2						endocytosis|intracellular protein transport|regulation of endocytosis	clathrin adaptor complex|nucleolus	protein binding			skin(3)|pancreas(2)	5				BRCA - Breast invasive adenocarcinoma(234;0.0348)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	82581361	82581362	+	IGR	INS	-	CA	CA			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82581361_82581362insCA								SEL1L (581156 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	83114656	83114656	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:83114656delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	83604825	83604825	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:83604825delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	84743088	84743091	+	IGR	DEL	TCCT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:84743088_84743091delTCCT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	84923132	84923132	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:84923132delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	85561623	85561624	+	IGR	INS	-	CA	CA	rs142577846	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:85561623_85561624insCA								None (None upstream) : FLRT2 (434864 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	85613509	85613509	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:85613509delA								None (None upstream) : FLRT2 (382979 downstream)																																			---	---	---	---
FLRT2	23768	broad.mit.edu	37	14	86058724	86058725	+	Intron	INS	-	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86058724_86058725insC	uc001xvr.2	+						FLRT2_uc010atd.2_Intron	NM_013231	NP_037363			fibronectin leucine rich transmembrane protein 2						cell adhesion	integral to plasma membrane|proteinaceous extracellular matrix	protein binding, bridging|receptor signaling protein activity			ovary(3)|haematopoietic_and_lymphoid_tissue(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.0319)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	86376428	86376428	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86376428delT								FLRT2 (282159 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	89418206	89418207	+	IGR	INS	-	AAC	AAC			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89418206_89418207insAAC								TTC8 (73872 upstream) : FOXN3 (204310 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	89542844	89542844	+	IGR	DEL	A	-	-	rs77023841		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89542844delA								TTC8 (198510 upstream) : FOXN3 (79673 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	89615909	89615912	+	IGR	DEL	AGAC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89615909_89615912delAGAC								TTC8 (271575 upstream) : FOXN3 (6605 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	90197470	90197470	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90197470delT								FOXN3 (111976 upstream) : C14orf143 (66001 downstream)																																			---	---	---	---
TDP1	55775	broad.mit.edu	37	14	90442027	90442027	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90442027delA	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	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	90858005	90858005	+	IGR	DEL	A	-	-	rs34924005		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90858005delA								C14orf102 (59726 upstream) : CALM1 (5368 downstream)																																			---	---	---	---
RPS6KA5	9252	broad.mit.edu	37	14	91490553	91490553	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91490553delT	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)														---	---	---	---
SMEK1	55671	broad.mit.edu	37	14	91927540	91927540	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91927540delA	uc001xzn.2	-						SMEK1_uc001xzm.2_Intron|SMEK1_uc001xzo.2_Intron|SMEK1_uc010atz.2_Intron	NM_032560	NP_115949			SMEK homolog 1, suppressor of mek1							microtubule organizing center|nucleus	protein binding				0		all_cancers(154;0.0691)|all_epithelial(191;0.219)		COAD - Colon adenocarcinoma(157;0.221)														---	---	---	---
TRIP11	9321	broad.mit.edu	37	14	92461661	92461661	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92461661delT	uc001xzy.2	-						TRIP11_uc010auf.1_Intron	NM_004239	NP_004230			thyroid hormone receptor interactor 11						transcription from RNA polymerase II promoter	cytoskeleton|Golgi apparatus|membrane|nucleus	protein binding|transcription coactivator activity			ovary(6)|skin(2)|kidney(2)|central_nervous_system(1)|lung(1)|breast(1)	13				COAD - Colon adenocarcinoma(157;0.223)				T	PDGFRB	AML								---	---	---	---
TRIP11	9321	broad.mit.edu	37	14	92493257	92493257	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92493257delA	uc001xzy.2	-							NM_004239	NP_004230			thyroid hormone receptor interactor 11						transcription from RNA polymerase II promoter	cytoskeleton|Golgi apparatus|membrane|nucleus	protein binding|transcription coactivator activity			ovary(6)|skin(2)|kidney(2)|central_nervous_system(1)|lung(1)|breast(1)	13				COAD - Colon adenocarcinoma(157;0.223)				T	PDGFRB	AML								---	---	---	---
SLC24A4	123041	broad.mit.edu	37	14	92815509	92815509	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92815509delT	uc001yak.2	+						SLC24A4_uc001yai.2_Intron|SLC24A4_uc010twm.1_Intron|SLC24A4_uc001yaj.2_Intron	NM_153646	NP_705932			solute carrier family 24 member 4 isoform 1							integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			breast(2)|ovary(1)	3		all_cancers(154;0.0347)|all_epithelial(191;0.163)		Colorectal(1;0.00242)|COAD - Colon adenocarcinoma(157;0.047)|Epithelial(152;0.0781)|READ - Rectum adenocarcinoma(1;0.176)|all cancers(159;0.182)														---	---	---	---
RIN3	79890	broad.mit.edu	37	14	93027839	93027839	+	Intron	DEL	T	-	-	rs36081705		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93027839delT	uc001yap.2	+						RIN3_uc010auk.2_Intron	NM_024832	NP_079108			Ras and Rab interactor 3						endocytosis|signal transduction	cytoplasmic membrane-bounded vesicle|early endosome	GTPase activator activity|Ras GTPase binding			lung(2)|ovary(1)	3		all_cancers(154;0.0701)																---	---	---	---
KIAA1409	57578	broad.mit.edu	37	14	93857622	93857622	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93857622delA	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)														---	---	---	---
KIAA1409	57578	broad.mit.edu	37	14	94084806	94084806	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94084806delA	uc001ybv.1	+						KIAA1409_uc001ybs.1_Intron	NM_020818	NP_065869			hypothetical protein LOC57578							integral to membrane				ovary(10)|skin(4)|large_intestine(3)	17		all_cancers(154;0.0354)|all_epithelial(191;0.216)		Epithelial(152;0.188)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	94832465	94832465	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94832465delT								SERPINA6 (42777 upstream) : SERPINA1 (10620 downstream)																																			---	---	---	---
SERPINA12	145264	broad.mit.edu	37	14	94968362	94968363	+	Intron	DEL	TG	-	-	rs34819811		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94968362_94968363delTG	uc001ydj.2	-							NM_173850	NP_776249			serine (or cysteine) proteinase inhibitor, clade						regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			central_nervous_system(2)|ovary(1)|lung(1)	4				COAD - Colon adenocarcinoma(157;0.235)														---	---	---	---
DICER1	23405	broad.mit.edu	37	14	95554260	95554260	+	3'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95554260delT	uc001ydw.2	-	28					DICER1_uc010avh.1_3'UTR|DICER1_uc001ydv.2_3'UTR|DICER1_uc001ydx.2_3'UTR	NM_030621	NP_085124			dicer1						negative regulation of Schwann cell proliferation|negative regulation of transcription from RNA polymerase II promoter|nerve development|neuron projection morphogenesis|peripheral nervous system myelin formation|positive regulation of myelination|positive regulation of Schwann cell differentiation|pre-miRNA processing|production of siRNA involved in RNA interference|targeting of mRNA for destruction involved in RNA interference	cytosol|RNA-induced silencing complex	ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity			skin(2)|ovary(1)|pancreas(1)|lung(1)	5		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)				Mis F|N			pleuropulmonary blastoma			DICER_1_syndrome_|Familial_Multinodular_Goiter_				---	---	---	---
Unknown	0	broad.mit.edu	37	14	95841286	95841287	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95841286_95841287insT								CLMN (55041 upstream) : C14orf139 (32319 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	97967888	97967888	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97967888delC								VRK1 (619938 upstream) : C14orf64 (424059 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	98334901	98334901	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98334901delT								VRK1 (986951 upstream) : C14orf64 (57046 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	98959964	98959964	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98959964delG								C14orf64 (515503 upstream) : C14orf177 (217986 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	98982249	98982250	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98982249_98982250delTT								C14orf64 (537788 upstream) : C14orf177 (195700 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	98985337	98985337	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98985337delA								C14orf64 (540876 upstream) : C14orf177 (192613 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	99437426	99437426	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99437426delT								C14orf177 (253329 upstream) : BCL11B (198201 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	100087445	100087445	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100087445delT								CCDC85C (16718 upstream) : HHIPL1 (24035 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	100430785	100430785	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100430785delA								EML1 (22392 upstream) : EVL (7366 downstream)																																			---	---	---	---
WARS	7453	broad.mit.edu	37	14	100833386	100833387	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100833386_100833387delAA	uc001yhf.1	-						WARS_uc001yhg.1_Intron|WARS_uc001yhh.1_Intron|WARS_uc001yhi.1_Intron|WARS_uc001yhj.1_Intron|WARS_uc001yhk.1_Intron|WARS_uc001yhl.1_Intron|WARS_uc010twz.1_Intron	NM_173701	NP_776049			tryptophanyl-tRNA synthetase isoform a						angiogenesis|negative regulation of cell proliferation|regulation of angiogenesis|tryptophanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|protein binding|tryptophan-tRNA ligase activity			breast(1)	1		all_cancers(154;0.00223)|all_lung(585;2.48e-06)|all_epithelial(191;0.000564)|Melanoma(154;0.152)			L-Tryptophan(DB00150)													---	---	---	---
Unknown	0	broad.mit.edu	37	14	101377646	101377646	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101377646delT								MIR370 (96 upstream) : SNORD113-1 (13512 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	101528241	101528242	+	5'Flank	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101528241_101528242delAG	uc010awh.1	+						MIR377_hsa-mir-377|MI0000785_5'Flank|MIR541_hsa-mir-541|MI0005539_5'Flank					DM004799																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	101623630	101623630	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101623630delT								MIR656 (90492 upstream) : DIO3OS (394930 downstream)																																			---	---	---	---
DYNC1H1	1778	broad.mit.edu	37	14	102442248	102442250	+	Intron	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102442248_102442250delTTT	uc001yks.2	+							NM_001376	NP_001367			cytoplasmic dynein 1 heavy chain 1						cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	centrosome|cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10																		---	---	---	---
WDR20	91833	broad.mit.edu	37	14	102631977	102631978	+	Intron	INS	-	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102631977_102631978insC	uc001ykz.2	+						WDR20_uc001yky.1_Intron|WDR20_uc001yla.2_Intron|WDR20_uc001ylb.2_Intron|WDR20_uc010txu.1_Intron|WDR20_uc001ylc.2_Intron|WDR20_uc001yld.2_Intron|WDR20_uc001yle.2_Intron|WDR20_uc001ylf.2_Intron	NM_144574	NP_653175			WD repeat domain 20 isoform 2												0																		---	---	---	---
KIF26A	26153	broad.mit.edu	37	14	104624142	104624142	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104624142delC	uc001yos.3	+	4	786	c.786delC	c.(784-786)TGCfs	p.C262fs		NM_015656	NP_056471	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	262					blood coagulation|enteric nervous system development|microtubule-based movement|negative regulation of signal transduction|regulation of cell growth by extracellular stimulus	cytosol|microtubule	ATP binding|microtubule binding|microtubule motor activity			pancreas(1)	1		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)	Epithelial(152;0.161)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	104873515	104873516	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104873515_104873516insA								KIF26A (226281 upstream) : C14orf180 (172540 downstream)																																			---	---	---	---
KIAA0284	283638	broad.mit.edu	37	14	105336446	105336447	+	Intron	INS	-	A	A	rs145345048	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105336446_105336447insA	uc010axb.2	+						INF2_uc010tyi.1_Intron|KIAA0284_uc001ypr.2_Intron	NM_001112726	NP_001106197			hypothetical protein LOC283638 isoform 1							cytoplasm|microtubule				breast(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000472)|OV - Ovarian serous cystadenocarcinoma(23;0.00596)|Epithelial(46;0.0149)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.178)														---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106866273	106866273	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106866273delT	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	20010729	20010730	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20010729_20010730insT								None (None upstream) : GOLGA6L6 (726364 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20445155	20445155	+	IGR	DEL	A	-	-	rs145123737		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20445155delA								None (None upstream) : GOLGA6L6 (291939 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20468324	20468324	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20468324delT								None (None upstream) : GOLGA6L6 (268770 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20522306	20522308	+	IGR	DEL	AAG	-	-	rs71758034		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20522306_20522308delAAG								None (None upstream) : GOLGA6L6 (214786 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20548998	20548998	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20548998delA								None (None upstream) : GOLGA6L6 (188096 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20552398	20552401	+	IGR	DEL	CTCA	-	-	rs34654161		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20552398_20552401delCTCA								None (None upstream) : GOLGA6L6 (184693 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	21919612	21919612	+	IGR	DEL	T	-	-	rs5811263		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21919612delT								NF1P1 (784987 upstream) : LOC646214 (12902 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	21961788	21961788	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21961788delA								LOC646214 (21049 upstream) : CXADRP2 (52632 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	22519155	22519155	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22519155delA								MIR1268 (5875 upstream) : GOLGA8DP (183130 downstream)																																			---	---	---	---
CYFIP1	23191	broad.mit.edu	37	15	22939037	22939037	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22939037delT	uc001yus.2	+						CYFIP1_uc001yut.2_Intron|CYFIP1_uc010aya.1_Intron	NM_014608	NP_055423			cytoplasmic FMR1 interacting protein 1 isoform						axon extension|lamellipodium assembly|regulation of cell shape|ruffle organization	cell junction|lamellipodium|mRNA cap binding complex|perinuclear region of cytoplasm|ruffle|synapse|synaptosome	actin filament binding|Rac GTPase binding			ovary(4)|pancreas(3)|liver(1)|skin(1)	9		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)														---	---	---	---
HERC2P2	400322	broad.mit.edu	37	15	23299147	23299147	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23299147delA	uc001yvq.2	-						HERC2P2_uc001yvo.3_Intron|HERC2P2_uc001yvp.3_Intron					Homo sapiens mRNA for KIAA0393 protein, partial cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	24218493	24218493	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24218493delA								NDN (286043 upstream) : PWRN2 (191433 downstream)																																			---	---	---	---
PWRN1	791114	broad.mit.edu	37	15	24780958	24780959	+	Intron	INS	-	AC	AC	rs144876699	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24780958_24780959insAC	uc001ywm.2	+											Homo sapiens cDNA FLJ25418 fis, clone TST03512.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	24974640	24974640	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24974640delT								C15orf2 (46048 upstream) : SNRPN (94154 downstream)																																			---	---	---	---
SNRPN	6638	broad.mit.edu	37	15	25126516	25126516	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25126516delA	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				---	---	---	---
UBE3A	7337	broad.mit.edu	37	15	25600932	25600932	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25600932delT	uc001zaq.2	-						uc001zae.2_Intron|UBE3A_uc001zar.2_Intron|UBE3A_uc001zas.2_Intron|UBE3A_uc001zat.2_Intron	NM_000462	NP_000453			ubiquitin protein ligase E3A isoform 2						brain development|interspecies interaction between organisms|protein K48-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity			upper_aerodigestive_tract(1)|ovary(1)|breast(1)	3		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	26432852	26432852	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26432852delT								ATP10A (322535 upstream) : GABRB3 (355843 downstream)																																			---	---	---	---
GABRB3	2562	broad.mit.edu	37	15	26923711	26923712	+	Intron	DEL	GA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26923711_26923712delGA	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	26960259	26960259	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26960259delG	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	27123663	27123663	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27123663delA	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)													---	---	---	---
GABRG3	2567	broad.mit.edu	37	15	27333035	27333036	+	Intron	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27333035_27333036delGT	uc001zbg.1	+						GABRG3_uc001zbf.2_Intron	NM_033223	NP_150092			gamma-aminobutyric acid (GABA) A receptor, gamma						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity				0		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	27810082	27810083	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27810082_27810083delAC								GABRG3 (31948 upstream) : OCA2 (189942 downstream)																																			---	---	---	---
HERC2	8924	broad.mit.edu	37	15	28387888	28387889	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28387888_28387889delAC	uc001zbj.2	-							NM_004667	NP_004658			hect domain and RLD 2						DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)														---	---	---	---
HERC2	8924	broad.mit.edu	37	15	28441817	28441817	+	Intron	DEL	G	-	-	rs2525936	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28441817delG	uc001zbj.2	-						HERC2_uc001zbk.1_Intron	NM_004667	NP_004658			hect domain and RLD 2						DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)														---	---	---	---
FAM189A1	23359	broad.mit.edu	37	15	29666851	29666851	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29666851delT	uc010azk.1	-							NM_015307	NP_056122			hypothetical protein LOC23359							integral to membrane					0																		---	---	---	---
FAM189A1	23359	broad.mit.edu	37	15	29755741	29755742	+	Intron	DEL	GA	-	-	rs147133405		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29755741_29755742delGA	uc010azk.1	-							NM_015307	NP_056122			hypothetical protein LOC23359							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	30220318	30220318	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30220318delA								TJP1 (105612 upstream) : FAM7A3 (175617 downstream)																																			---	---	---	---
OTUD7A	161725	broad.mit.edu	37	15	32047207	32047208	+	Intron	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32047207_32047208delAG	uc001zfr.2	-						OTUD7A_uc001zfs.1_Intron|OTUD7A_uc010baa.1_Intron	NM_130901	NP_570971			OTU domain containing 7A							cytoplasm|nucleus	cysteine-type peptidase activity|DNA binding|zinc ion binding			pancreas(1)|skin(1)	2		all_lung(180;1.6e-09)		all cancers(64;2.44e-19)|Epithelial(43;6.82e-14)|GBM - Glioblastoma multiforme(186;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00189)|Lung(196;0.208)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	32301476	32301477	+	IGR	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32301476_32301477delGT								OTUD7A (138484 upstream) : CHRNA7 (21249 downstream)																																			---	---	---	---
CHRNA7	1139	broad.mit.edu	37	15	32409252	32409252	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32409252delG	uc001zft.2	+						CHRNA7_uc010bae.1_Intron|CHRNA7_uc010baf.2_Intron|CHRNA7_uc010bah.1_Intron|CHRNA7_uc010bai.1_Intron|CHRNA7_uc010baj.1_Intron|CHRNA7_uc010bak.2_Intron	NM_000746	NP_000737			cholinergic receptor, nicotinic, alpha 7						activation of MAPK activity|calcium ion transport|cellular calcium ion homeostasis|memory|negative regulation of tumor necrosis factor production|positive regulation of angiogenesis|positive regulation of cell proliferation|response to hypoxia|response to nicotine	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|beta-amyloid binding|chloride channel regulator activity|nicotinic acetylcholine-activated cation-selective channel activity|protein homodimerization activity|toxin binding			ovary(1)	1		all_lung(180;6.35e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)	Nicotine(DB00184)|Varenicline(DB01273)													---	---	---	---
RYR3	6263	broad.mit.edu	37	15	33833295	33833295	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33833295delT	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	34157542	34157543	+	3'UTR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34157542_34157543delAA	uc001zhi.2	+	104					RYR3_uc010bar.2_3'UTR	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)														---	---	---	---
SLC12A6	9990	broad.mit.edu	37	15	34528550	34528550	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34528550delT	uc001zhw.2	-						SLC12A6_uc001zhv.2_Intron|SLC12A6_uc001zhx.2_Intron|SLC12A6_uc001zhy.2_Intron|SLC12A6_uc001zhz.2_Intron|SLC12A6_uc001zia.2_Intron|SLC12A6_uc001zib.2_Intron|SLC12A6_uc001zic.2_Intron|SLC12A6_uc010bau.2_Intron|SLC12A6_uc001zid.2_Intron|SLC12A6_uc001zht.2_Intron|SLC12A6_uc001zhu.2_Intron	NM_133647	NP_598408			solute carrier family 12, member 6 isoform a						angiogenesis|cellular hypotonic salinity response|potassium ion transport|sodium ion transport	basolateral plasma membrane|integral to membrane	potassium:chloride symporter activity			central_nervous_system(5)|ovary(1)|skin(1)	7		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)													---	---	---	---
Unknown	0	broad.mit.edu	37	15	35055106	35055106	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35055106delG	uc001zit.1	+											Homo sapiens cDNA FLJ34768 fis, clone NT2NE2002791.																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	35144376	35144378	+	IGR	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35144376_35144378delTTT								ACTC1 (56449 upstream) : AQR (4175 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	36011005	36011005	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:36011005delT	uc001zjc.2	+											Homo sapiens, Similar to LOC161538, clone IMAGE:5199550, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	36230679	36230679	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:36230679delT								ATPBD4 (392275 upstream) : C15orf41 (641133 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	36326298	36326298	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:36326298delA								ATPBD4 (487894 upstream) : C15orf41 (545514 downstream)																																			---	---	---	---
C15orf41	84529	broad.mit.edu	37	15	36870474	36870474	+	5'Flank	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:36870474delG	uc001zje.3	+						C15orf41_uc001zjd.2_5'Flank	NM_001130010	NP_001123482			hypothetical protein LOC84529 isoform 1								protein binding			pancreas(1)	1		all_epithelial(112;3.06e-10)|Lung NSC(122;6.48e-08)|all_lung(180;8.31e-07)|Melanoma(134;0.222)		all cancers(64;1.76e-19)|GBM - Glioblastoma multiforme(113;5.03e-07)|BRCA - Breast invasive adenocarcinoma(123;0.11)														---	---	---	---
LOC145845	145845	broad.mit.edu	37	15	37176293	37176294	+	Intron	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37176293_37176294delTC	uc001zji.2	-							NR_024264				Homo sapiens cDNA FLJ13192 fis, clone NT2RP3004341.												0																OREG0023041	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
MEIS2	4212	broad.mit.edu	37	15	37378312	37378312	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37378312delT	uc001zjr.2	-						MEIS2_uc001zjl.2_Intron|MEIS2_uc010ucj.1_Intron|MEIS2_uc001zjm.2_Intron|MEIS2_uc001zjn.2_Intron|MEIS2_uc001zjo.2_Intron|MEIS2_uc001zjp.2_Intron|MEIS2_uc001zjs.2_Intron|MEIS2_uc001zju.2_Intron|MEIS2_uc001zjt.2_Intron	NM_170675	NP_733775			Meis homeobox 2 isoform c						negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(2)	2		all_epithelial(112;9.77e-14)|Lung NSC(122;1.42e-09)|all_lung(180;2.2e-08)|Ovarian(310;0.134)|Melanoma(134;0.155)		all cancers(64;9.33e-21)|GBM - Glioblastoma multiforme(113;1.71e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0288)														---	---	---	---
SPRED1	161742	broad.mit.edu	37	15	38556013	38556013	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38556013delA	uc001zka.3	+							NM_152594	NP_689807			sprouty-related protein 1 with EVH-1 domain						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				---	---	---	---
Unknown	0	broad.mit.edu	37	15	38700315	38700315	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38700315delT								SPRED1 (50866 upstream) : FAM98B (46013 downstream)																																			---	---	---	---
RASGRP1	10125	broad.mit.edu	37	15	38792546	38792549	+	Intron	DEL	TTTG	-	-	rs12904148	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38792546_38792549delTTTG	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	39216771	39216771	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39216771delT								C15orf53 (224532 upstream) : C15orf54 (326114 downstream)																																			---	---	---	---
FSIP1	161835	broad.mit.edu	37	15	40014822	40014823	+	Intron	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40014822_40014823delCT	uc001zki.2	-							NM_152597	NP_689810			fibrous sheath interacting protein 1											ovary(2)|skin(1)	3		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)														---	---	---	---
BUB1B	701	broad.mit.edu	37	15	40484062	40484063	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40484062_40484063delTT	uc001zkx.3	+						BUB1B_uc010ucl.1_Intron	NM_001211	NP_001202			budding uninhibited by benzimidazoles 1 beta						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell division|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|phosphatidylinositol-mediated signaling|protein localization to kinetochore|spindle organization	anaphase-promoting complex|condensed chromosome outer kinetochore|cytosol|microtubule organizing center|perinuclear region of cytoplasm|spindle midzone	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(2)|ovary(1)|kidney(1)	4		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)				Mis|N|F|S			rhabdomyosarcoma			Mosaic_Variegated_Aneuploidy_Syndrome				---	---	---	---
BUB1B	701	broad.mit.edu	37	15	40491591	40491591	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40491591delT	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				---	---	---	---
Unknown	0	broad.mit.edu	37	15	40775479	40775480	+	IGR	INS	-	TT	TT	rs10636995		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40775479_40775480insTT								CHST14 (10126 upstream) : MRPL42P5 (48060 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	41263159	41263159	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41263159delA								CHAC1 (14442 upstream) : INO80 (7922 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	41460585	41460586	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41460585_41460586delTT								INO80 (52245 upstream) : EXD1 (14347 downstream)																																			---	---	---	---
EXD1	161829	broad.mit.edu	37	15	41483956	41483956	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41483956delA	uc001znk.2	-						EXD1_uc001znj.2_5'Flank|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																		---	---	---	---
CHP	11261	broad.mit.edu	37	15	41559868	41559868	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41559868delA	uc001znl.2	+							NM_007236	NP_009167			calcium binding protein P22						potassium ion transport|small GTPase mediated signal transduction		potassium channel regulator activity			ovary(1)	1		all_cancers(109;1.19e-18)|all_epithelial(112;5.87e-16)|Lung NSC(122;8.86e-12)|all_lung(180;2.47e-10)|Melanoma(134;0.0574)|Colorectal(260;0.0946)|Ovarian(310;0.143)		GBM - Glioblastoma multiforme(113;1.68e-06)|LUSC - Lung squamous cell carcinoma(244;0.008)|Lung(196;0.00802)|BRCA - Breast invasive adenocarcinoma(123;0.169)														---	---	---	---
LOC729082	729082	broad.mit.edu	37	15	41590298	41590299	+	RNA	INS	-	T	T	rs149103084	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41590298_41590299insT	uc001znm.3	+	4		c.397_398insT			LOC729082_uc001znn.1_Intron	NR_026757				Homo sapiens cDNA FLJ26241 fis, clone DMC00738.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	41895345	41895346	+	IGR	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41895345_41895346delGT								TYRO3 (23819 upstream) : MGA (18418 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	41905920	41905920	+	IGR	DEL	C	-	-	rs146607222		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41905920delC								TYRO3 (34394 upstream) : MGA (7844 downstream)																																			---	---	---	---
MGA	23269	broad.mit.edu	37	15	41978992	41978993	+	Intron	DEL	GA	-	-	rs75116764	byFrequency;by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41978992_41978993delGA	uc001zog.1	+						MGA_uc010ucy.1_Intron|MGA_uc010ucz.1_Intron	NM_001080541	NP_001074010			MAX-interacting protein isoform 2							MLL1 complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	12		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)														---	---	---	---
MGA	23269	broad.mit.edu	37	15	41989340	41989340	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41989340delG	uc001zog.1	+						MGA_uc010ucy.1_Intron|MGA_uc010ucz.1_Intron	NM_001080541	NP_001074010			MAX-interacting protein isoform 2							MLL1 complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	12		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)														---	---	---	---
MGA	23269	broad.mit.edu	37	15	41999828	41999828	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41999828delC	uc001zog.1	+						MGA_uc010ucy.1_Intron|MGA_uc010ucz.1_Intron	NM_001080541	NP_001074010			MAX-interacting protein isoform 2							MLL1 complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	12		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)														---	---	---	---
EHD4	30844	broad.mit.edu	37	15	42221838	42221839	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42221838_42221839insA	uc001zot.2	-							NM_139265	NP_644670			EH-domain containing 4						endocytic recycling|protein homooligomerization	early endosome membrane|endoplasmic reticulum|nucleus|recycling endosome membrane	ATP binding|calcium ion binding|GTP binding|GTPase activity|nucleic acid binding|protein binding			ovary(2)	2		all_cancers(109;2.54e-12)|all_epithelial(112;6.59e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)		OV - Ovarian serous cystadenocarcinoma(18;1.6e-19)|GBM - Glioblastoma multiforme(94;3.77e-06)|COAD - Colon adenocarcinoma(120;0.0474)|Colorectal(105;0.0538)														---	---	---	---
EHD4	30844	broad.mit.edu	37	15	42246839	42246839	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42246839delT	uc001zot.2	-						EHD4_uc001zou.2_Intron	NM_139265	NP_644670			EH-domain containing 4						endocytic recycling|protein homooligomerization	early endosome membrane|endoplasmic reticulum|nucleus|recycling endosome membrane	ATP binding|calcium ion binding|GTP binding|GTPase activity|nucleic acid binding|protein binding			ovary(2)	2		all_cancers(109;2.54e-12)|all_epithelial(112;6.59e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)		OV - Ovarian serous cystadenocarcinoma(18;1.6e-19)|GBM - Glioblastoma multiforme(94;3.77e-06)|COAD - Colon adenocarcinoma(120;0.0474)|Colorectal(105;0.0538)														---	---	---	---
ZFP106	64397	broad.mit.edu	37	15	42721641	42721641	+	Intron	DEL	A	-	-	rs77454804		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42721641delA	uc001zpw.2	-						ZFP106_uc001zpu.2_Intron|ZFP106_uc001zpv.2_Intron|ZFP106_uc001zpx.2_Intron	NM_022473	NP_071918			zinc finger protein 106 homolog							nucleolus	zinc ion binding			central_nervous_system(2)|ovary(1)	3		all_cancers(109;1.63e-12)|all_epithelial(112;3.97e-11)|Lung NSC(122;2.04e-07)|all_lung(180;8.31e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.6e-07)														---	---	---	---
ZFP106	64397	broad.mit.edu	37	15	42747097	42747097	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42747097delA	uc001zpw.2	-						ZFP106_uc001zpv.2_Intron|ZFP106_uc001zpx.2_Intron|ZFP106_uc010udh.1_Intron|ZFP106_uc001zpy.1_Intron	NM_022473	NP_071918			zinc finger protein 106 homolog							nucleolus	zinc ion binding			central_nervous_system(2)|ovary(1)	3		all_cancers(109;1.63e-12)|all_epithelial(112;3.97e-11)|Lung NSC(122;2.04e-07)|all_lung(180;8.31e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.6e-07)														---	---	---	---
TTBK2	146057	broad.mit.edu	37	15	43089847	43089847	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43089847delT	uc001zqo.2	-						TTBK2_uc010bcy.2_Intron|TTBK2_uc001zqp.2_Intron|TTBK2_uc010bcz.1_Intron	NM_173500	NP_775771			tau tubulin kinase 2						cell death		ATP binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|stomach(1)|pancreas(1)|skin(1)	7		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;3.23e-07)														---	---	---	---
UBR1	197131	broad.mit.edu	37	15	43283474	43283474	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43283474delA	uc001zqq.2	-							NM_174916	NP_777576			ubiquitin protein ligase E3 component n-recognin						cellular response to leucine|negative regulation of TOR signaling cascade	cytosol	leucine binding|zinc ion binding			lung(1)	1		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)														---	---	---	---
UBR1	197131	broad.mit.edu	37	15	43283804	43283804	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43283804delA	uc001zqq.2	-							NM_174916	NP_777576			ubiquitin protein ligase E3 component n-recognin						cellular response to leucine|negative regulation of TOR signaling cascade	cytosol	leucine binding|zinc ion binding			lung(1)	1		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)														---	---	---	---
TMEM62	80021	broad.mit.edu	37	15	43445414	43445415	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43445414_43445415delTT	uc001zqr.2	+						TMEM62_uc010bda.2_Intron	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)														---	---	---	---
TUBGCP4	27229	broad.mit.edu	37	15	43669990	43669990	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43669990delT	uc001zro.2	+						TUBGCP4_uc001zrn.2_Intron|TUBGCP4_uc010bdh.2_Intron	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)														---	---	---	---
TUBGCP4	27229	broad.mit.edu	37	15	43676006	43676007	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43676006_43676007delTT	uc001zro.2	+						TUBGCP4_uc001zrn.2_Intron|TUBGCP4_uc010bdh.2_Intron	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)														---	---	---	---
CATSPER2P1	440278	broad.mit.edu	37	15	44034605	44034605	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44034605delA	uc001zss.2	-							NR_002318				Homo sapiens cation channel, sperm associated 2 pseudogene 1, mRNA (cDNA clone IMAGE:5294645).												0																		---	---	---	---
ELL3	80237	broad.mit.edu	37	15	44088620	44088620	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44088620delC	uc001zsx.1	-						C15orf63_uc001ztb.2_Intron|MIR1282_hsa-mir-1282|MI0006429_5'Flank|SERINC4_uc001ztc.1_Intron|SERINC4_uc001ztd.1_Intron|SERINC4_uc010bds.1_Intron|SERINC4_uc001zte.1_Intron	NM_025165	NP_079441			elongation factor RNA polymerase II-like 3						positive regulation of transcription elongation, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|spermatogenesis|transcription elongation from RNA polymerase II promoter	transcription elongation factor complex				ovary(1)	1		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;7.81e-07)														---	---	---	---
FRMD5	84978	broad.mit.edu	37	15	44413850	44413850	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44413850delA	uc001ztl.2	-						FRMD5_uc001ztk.1_Intron|FRMD5_uc001ztm.2_Intron|FRMD5_uc001ztn.2_Intron	NM_032892	NP_116281			FERM domain containing 5 isoform 2							cytoplasm|cytoskeleton|extrinsic to membrane|integral to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(109;2.29e-15)|all_epithelial(112;9.98e-13)|Lung NSC(122;4.89e-08)|all_lung(180;5.08e-07)|Melanoma(134;0.0275)		all cancers(107;8.63e-20)|GBM - Glioblastoma multiforme(94;3.63e-06)														---	---	---	---
CASC4	113201	broad.mit.edu	37	15	44594190	44594190	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44594190delA	uc001zto.1	+						CASC4_uc001ztp.2_Intron|CASC4_uc001ztq.2_Intron|CASC4_uc010bdu.1_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)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	45176545	45176546	+	IGR	INS	-	A	A	rs112641611		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45176545_45176546insA								TRIM69 (116520 upstream) : C15orf43 (72357 downstream)																																			---	---	---	---
SLC30A4	7782	broad.mit.edu	37	15	45782231	45782231	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45782231delA	uc001zvj.2	-							NM_013309	NP_037441			solute carrier family 30 (zinc transporter),						regulation of sequestering of zinc ion|response to toxin	endosome membrane|integral to membrane|late endosome	zinc ion transmembrane transporter activity				0		Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.58e-16)|GBM - Glioblastoma multiforme(94;2.15e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	45915191	45915191	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45915191delA								PLDN (13283 upstream) : SQRDL (8155 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	45984403	45984403	+	IGR	DEL	T	-	-	rs72086037		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45984403delT								SQRDL (925 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	46077614	46077614	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:46077614delT								SQRDL (94136 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	46570085	46570085	+	IGR	DEL	T	-	-	rs72146513		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:46570085delT								SQRDL (586607 upstream) : SEMA6D (906318 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	46757599	46757601	+	IGR	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:46757599_46757601delAAA								SQRDL (774121 upstream) : SEMA6D (718802 downstream)																																			---	---	---	---
SLC12A1	6557	broad.mit.edu	37	15	48593699	48593700	+	Intron	INS	-	G	G	rs60810487		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48593699_48593700insG	uc001zwn.3	+						SLC12A1_uc001zwq.3_Intron|SLC12A1_uc001zwr.3_Intron	NM_000338	NP_000329			sodium potassium chloride cotransporter 2						potassium ion transport|sodium ion transport	integral to membrane|membrane fraction	sodium:potassium:chloride symporter activity			ovary(1)|central_nervous_system(1)	2		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Metolazone(DB00524)|Potassium Chloride(DB00761)|Torasemide(DB00214)|Trichlormethiazide(DB01021)													---	---	---	---
FBN1	2200	broad.mit.edu	37	15	48872241	48872241	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48872241delA	uc001zwx.1	-							NM_000138	NP_000129			fibrillin 1 precursor						heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development	basement membrane|extracellular space|microfibril	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(2)|large_intestine(1)	3		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)														---	---	---	---
FBN1	2200	broad.mit.edu	37	15	48915521	48915521	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48915521delA	uc001zwx.1	-							NM_000138	NP_000129			fibrillin 1 precursor						heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development	basement membrane|extracellular space|microfibril	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(2)|large_intestine(1)	3		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)														---	---	---	---
CEP152	22995	broad.mit.edu	37	15	49059021	49059021	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49059021delA	uc001zwy.2	-						CEP152_uc001zwz.2_Intron|CEP152_uc001zxa.1_Intron	NM_014985	NP_055800			centrosomal protein 152kDa						centrosome duplication|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein kinase binding			lung(2)	2		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	50018440	50018440	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50018440delA								DTWD1 (81108 upstream) : ATP8B4 (131996 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	50136047	50136047	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50136047delC								DTWD1 (198715 upstream) : ATP8B4 (14389 downstream)																																			---	---	---	---
SPPL2A	84888	broad.mit.edu	37	15	51011450	51011450	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51011450delT	uc001zyv.2	-							NM_032802	NP_116191			signal peptide peptidase-like 2A							integral to membrane	aspartic-type endopeptidase activity				0				all cancers(107;0.000712)|GBM - Glioblastoma multiforme(94;0.00314)														---	---	---	---
SPPL2A	84888	broad.mit.edu	37	15	51011920	51011921	+	Intron	DEL	TT	-	-	rs67581503		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51011920_51011921delTT	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)														---	---	---	---
AP4E1	23431	broad.mit.edu	37	15	51285872	51285872	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51285872delA	uc001zyx.1	+							NM_007347	NP_031373			adaptor-related protein complex 4, epsilon 1						intracellular protein transport|vesicle-mediated transport	COPI vesicle coat	binding|structural molecule activity				0				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	51445614	51445614	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51445614delT								TNFAIP8L3 (48141 upstream) : CYP19A1 (54641 downstream)																																			---	---	---	---
DMXL2	23312	broad.mit.edu	37	15	51757639	51757640	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51757639_51757640delTT	uc002abf.2	-						DMXL2_uc002abd.2_Intron|DMXL2_uc010ufy.1_Intron|DMXL2_uc010bfa.2_Intron	NM_015263	NP_056078			Dmx-like 2							cell junction|synaptic vesicle membrane	Rab GTPase binding			ovary(6)|skin(3)	9				all cancers(107;0.00494)														---	---	---	---
MYO5A	4644	broad.mit.edu	37	15	52606060	52606060	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52606060delA	uc002aby.2	-						MYO5A_uc002abx.3_Intron|MYO5A_uc010ugd.1_Intron	NM_000259	NP_000250			myosin VA isoform 1						actin filament-based movement|transport	cytoplasm|growth cone|myosin complex|ruffle	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|central_nervous_system(1)	4				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	53585472	53585473	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53585472_53585473insA								ONECUT1 (503263 upstream) : WDR72 (220465 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	53698994	53698994	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53698994delA								ONECUT1 (616785 upstream) : WDR72 (106944 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	55298481	55298481	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55298481delT								UNC13C (377676 upstream) : RSL24D1 (175040 downstream)																																			---	---	---	---
CCPG1	9236	broad.mit.edu	37	15	55783155	55783155	+	Intron	DEL	A	-	-	rs74830467		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55783155delA	uc002acy.2	-						DYX1C1_uc010ugh.1_Intron|DYX1C1_uc010ugi.1_Intron|DYX1C1_uc002adb.2_Intron|DYX1C1_uc002adc.2_Intron|DYX1C1_uc002add.2_Intron	NM_020739	NP_065790			cell cycle progression 1 isoform 2						cell cycle	integral to membrane				ovary(1)	1				all cancers(107;0.0354)														---	---	---	---
PYGO1	26108	broad.mit.edu	37	15	55844391	55844391	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55844391delA	uc010bfl.1	-						PYGO1_uc002adf.1_Intron	NM_015617	NP_056432			pygopus homolog 1						Wnt receptor signaling pathway	nucleus	zinc ion binding			ovary(1)|skin(1)	2				all cancers(107;0.0131)|GBM - Glioblastoma multiforme(80;0.18)														---	---	---	---
NEDD4	4734	broad.mit.edu	37	15	56275501	56275502	+	Intron	INS	-	GCGC	GCGC	rs139744104	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56275501_56275502insGCGC	uc002adl.2	-							NM_006154	NP_006145			neural precursor cell expressed, developmentally						development involved in symbiotic interaction|glucocorticoid receptor signaling pathway|negative regulation of sodium ion transport|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage|negative regulation of vascular endothelial growth factor receptor signaling pathway|neuron projection development|positive regulation of nucleocytoplasmic transport|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein catabolic process|progesterone receptor signaling pathway|protein K63-linked ubiquitination|protein targeting to lysosome|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|receptor internalization|regulation of dendrite morphogenesis|response to calcium ion|transmission of virus	apicolateral plasma membrane|cell cortex|chromatin|cytosol|perinuclear region of cytoplasm|ubiquitin ligase complex	beta-2 adrenergic receptor binding|phosphoserine binding|phosphothreonine binding|proline-rich region binding|protein domain specific binding|RNA polymerase binding|sodium channel inhibitor activity|ubiquitin binding|ubiquitin-protein ligase activity			skin(2)|ovary(1)|breast(1)	4				all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)														---	---	---	---
TCF12	6938	broad.mit.edu	37	15	57415850	57415850	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57415850delA	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								---	---	---	---
Unknown	0	broad.mit.edu	37	15	58152987	58152987	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58152987delT								GCOM1 (143235 upstream) : ALDH1A2 (92641 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	58630100	58630100	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58630100delG								ALDH1A2 (58638 upstream) : LIPC (72675 downstream)																																			---	---	---	---
LIPC	3990	broad.mit.edu	37	15	58837439	58837439	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58837439delT	uc010bga.1	+						LIPC_uc010bfz.1_Intron|LIPC_uc002afa.1_Intron|LIPC_uc010bgb.1_Intron|LIPC_uc010ugy.1_Intron	NM_000236	NP_000227			lipase C precursor						cholesterol homeostasis|chylomicron remnant clearance|fatty acid biosynthetic process|high-density lipoprotein particle remodeling|intermediate-density lipoprotein particle remodeling|low-density lipoprotein particle remodeling|phosphatidylcholine catabolic process|triglyceride catabolic process|triglyceride homeostasis|very-low-density lipoprotein particle remodeling	high-density lipoprotein particle	apolipoprotein binding|heparin binding|low-density lipoprotein particle binding|phospholipase activity|triglyceride lipase activity			ovary(1)	1		Colorectal(260;0.215)		GBM - Glioblastoma multiforme(80;0.00213)|all cancers(107;0.00548)														---	---	---	---
ADAM10	102	broad.mit.edu	37	15	58921980	58921980	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58921980delT	uc002afd.1	-						ADAM10_uc010bgc.1_Intron|ADAM10_uc010ugz.1_Intron|ADAM10_uc002afe.1_Intron	NM_001110	NP_001101			ADAM metallopeptidase domain 10 precursor						cell-cell signaling|constitutive protein ectodomain proteolysis|epidermal growth factor receptor signaling pathway|in utero embryonic development|integrin-mediated signaling pathway|monocyte activation|negative regulation of cell adhesion|Notch receptor processing|Notch signaling pathway|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of T cell chemotaxis|protein phosphorylation|response to tumor necrosis factor	cell surface|endomembrane system|Golgi-associated vesicle|integral to membrane|nucleus|plasma membrane	integrin binding|metalloendopeptidase activity|protein homodimerization activity|protein kinase binding|SH3 domain binding|zinc ion binding			skin(2)	2				GBM - Glioblastoma multiforme(80;0.202)														---	---	---	---
ADAM10	102	broad.mit.edu	37	15	58925364	58925364	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58925364delT	uc002afd.1	-						ADAM10_uc010bgc.1_Intron|ADAM10_uc010ugz.1_Intron|ADAM10_uc002afe.1_Intron	NM_001110	NP_001101			ADAM metallopeptidase domain 10 precursor						cell-cell signaling|constitutive protein ectodomain proteolysis|epidermal growth factor receptor signaling pathway|in utero embryonic development|integrin-mediated signaling pathway|monocyte activation|negative regulation of cell adhesion|Notch receptor processing|Notch signaling pathway|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of T cell chemotaxis|protein phosphorylation|response to tumor necrosis factor	cell surface|endomembrane system|Golgi-associated vesicle|integral to membrane|nucleus|plasma membrane	integrin binding|metalloendopeptidase activity|protein homodimerization activity|protein kinase binding|SH3 domain binding|zinc ion binding			skin(2)	2				GBM - Glioblastoma multiforme(80;0.202)														---	---	---	---
FAM63B	54629	broad.mit.edu	37	15	59107891	59107892	+	Intron	INS	-	T	T	rs34657462		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59107891_59107892insT	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	59186310	59186310	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59186310delT	uc002afp.2	-	11	1548	c.1460delA	c.(1459-1461)AATfs	p.N487fs	SLTM_uc002afn.2_Frame_Shift_Del_p.N56fs|SLTM_uc002afo.2_Frame_Shift_Del_p.N469fs|SLTM_uc002afq.2_Frame_Shift_Del_p.N56fs|SLTM_uc010bgd.2_Frame_Shift_Del_p.N56fs	NM_024755	NP_079031	Q9NWH9	SLTM_HUMAN	modulator of estrogen induced transcription	487					apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
MYO1E	4643	broad.mit.edu	37	15	59616180	59616182	+	Intron	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59616180_59616182delAAA	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)														---	---	---	---
BNIP2	663	broad.mit.edu	37	15	59967925	59967925	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59967925delA	uc010uhc.1	-						BNIP2_uc010uhb.1_Intron	NM_004330	NP_004321			BCL2/adenovirus E1B 19kD interacting protein 2						anti-apoptosis|apoptosis|positive regulation of muscle cell differentiation	nuclear envelope|perinuclear region of cytoplasm	calcium ion binding|GTPase activator activity|protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	60418054	60418054	+	IGR	DEL	A	-	-	rs79519694		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60418054delA								FOXB1 (89646 upstream) : ANXA2 (221297 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	61657877	61657877	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61657877delT								RORA (136375 upstream) : VPS13C (486715 downstream)																																			---	---	---	---
VPS13C	54832	broad.mit.edu	37	15	62221951	62221951	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62221951delA	uc002agz.2	-						VPS13C_uc002aha.2_Intron|VPS13C_uc002ahb.1_Intron|VPS13C_uc002ahc.1_Intron	NM_020821	NP_065872			vacuolar protein sorting 13C protein isoform 2A						protein localization					ovary(2)	2																		---	---	---	---
VPS13C	54832	broad.mit.edu	37	15	62254181	62254181	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62254181delT	uc002agz.2	-						VPS13C_uc002aha.2_Intron|VPS13C_uc002ahb.1_Intron|VPS13C_uc002ahc.1_Intron	NM_020821	NP_065872			vacuolar protein sorting 13C protein isoform 2A						protein localization					ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	62582781	62582781	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62582781delA								C2CD4B (125299 upstream) : MGC15885 (346590 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	62654132	62654132	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62654132delA								C2CD4B (196650 upstream) : MGC15885 (275239 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	62836376	62836376	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62836376delA								C2CD4B (378894 upstream) : MGC15885 (92995 downstream)																																			---	---	---	---
TLN2	83660	broad.mit.edu	37	15	62966785	62966785	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62966785delC	uc002alb.3	+							NM_015059	NP_055874			talin 2						cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(5)|upper_aerodigestive_tract(2)|lung(2)|breast(2)	11																		---	---	---	---
TLN2	83660	broad.mit.edu	37	15	63014438	63014438	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63014438delT	uc002alb.3	+							NM_015059	NP_055874			talin 2						cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(5)|upper_aerodigestive_tract(2)|lung(2)|breast(2)	11																		---	---	---	---
TLN2	83660	broad.mit.edu	37	15	63078040	63078040	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63078040delT	uc002alb.3	+						TLN2_uc002alc.3_Intron	NM_015059	NP_055874			talin 2						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	63298526	63298529	+	IGR	DEL	ACAT	-	-	rs10580376		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63298526_63298529delACAT								TLN2 (161699 upstream) : TPM1 (36309 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	63383060	63383060	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63383060delA								TPM1 (18949 upstream) : LACTB (30972 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	63392954	63392954	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63392954delT								TPM1 (28843 upstream) : LACTB (21078 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	63694673	63694673	+	IGR	DEL	T	-	-	rs75612693		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63694673delT								CA12 (20598 upstream) : USP3 (102137 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	63788347	63788347	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63788347delA								CA12 (114272 upstream) : USP3 (8463 downstream)																																			---	---	---	---
USP3	9960	broad.mit.edu	37	15	63812062	63812062	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63812062delT	uc002amf.2	+						USP3_uc010uii.1_Intron|USP3_uc002amg.2_Intron|USP3_uc002amh.2_Intron|USP3_uc010uij.1_Intron|USP3_uc010uik.1_Intron	NM_006537	NP_006528			ubiquitin thiolesterase 3						DNA repair|histone deubiquitination|mitotic cell cycle|regulation of protein stability|ubiquitin-dependent protein catabolic process	nuclear chromatin	histone binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(1)	1				GBM - Glioblastoma multiforme(80;0.0187)														---	---	---	---
HERC1	8925	broad.mit.edu	37	15	63923747	63923747	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63923747delT	uc002amp.2	-							NM_003922	NP_003913			hect domain and RCC1-like domain 1						protein modification process|transport	cytosol|Golgi apparatus|membrane	acid-amino acid ligase activity|ARF guanyl-nucleotide exchange factor activity			ovary(6)|breast(6)|lung(5)|central_nervous_system(2)	19																		---	---	---	---
PLEKHO2	80301	broad.mit.edu	37	15	65132402	65132403	+	5'Flank	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65132402_65132403delTT	uc002anv.2	+						PLEKHO2_uc010bgz.2_5'Flank|PLEKHO2_uc002anw.2_5'Flank	NM_025201	NP_079477			pleckstrin homology domain containing, family O											ovary(1)|lung(1)	2																		---	---	---	---
ANKDD1A	348094	broad.mit.edu	37	15	65245057	65245058	+	Intron	INS	-	CTC	CTC	rs148979860	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65245057_65245058insCTC	uc002aoa.2	+						ANKDD1A_uc002aoc.2_Intron|ANKDD1A_uc010bha.2_Intron	NM_182703	NP_874362			ankyrin repeat and death domain containing 1A						signal transduction					ovary(1)	1																		---	---	---	---
PDCD7	10081	broad.mit.edu	37	15	65428159	65428159	+	5'Flank	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65428159delA	uc002aol.2	-							NM_005707	NP_005698			programmed cell death 7						apoptosis|induction of apoptosis|response to glucocorticoid stimulus	U12-type spliceosomal complex					0																		---	---	---	---
PTPLAD1	51495	broad.mit.edu	37	15	65844283	65844283	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65844283delA	uc002apc.2	+						PTPLAD1_uc002apb.1_Intron|PTPLAD1_uc010uiw.1_Intron	NM_016395	NP_057479			protein tyrosine phosphatase-like A domain						activation of JUN kinase activity|fatty acid biosynthetic process|I-kappaB kinase/NF-kappaB cascade|Rac protein signal transduction	endoplasmic reticulum membrane|integral to membrane	GTPase activator activity|lyase activity|protein binding				0																		---	---	---	---
PTPLAD1	51495	broad.mit.edu	37	15	65860705	65860705	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65860705delT	uc002apc.2	+						PTPLAD1_uc002apb.1_Intron|PTPLAD1_uc010uiw.1_Intron	NM_016395	NP_057479			protein tyrosine phosphatase-like A domain						activation of JUN kinase activity|fatty acid biosynthetic process|I-kappaB kinase/NF-kappaB cascade|Rac protein signal transduction	endoplasmic reticulum membrane|integral to membrane	GTPase activator activity|lyase activity|protein binding				0																		---	---	---	---
PTPLAD1	51495	broad.mit.edu	37	15	65868695	65868695	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65868695delA	uc002apc.2	+	11	1215	c.1067delA	c.(1066-1068)CAAfs	p.Q356fs	PTPLAD1_uc010uiw.1_Frame_Shift_Del_p.Q301fs	NM_016395	NP_057479	Q9P035	HACD3_HUMAN	protein tyrosine phosphatase-like A domain	356	Cytoplasmic (Potential).			RRYGQKKKKIH -> LKMRAGAVAHACDPSALGG (in Ref. 1; CAB69070).	activation of JUN kinase activity|fatty acid biosynthetic process|I-kappaB kinase/NF-kappaB cascade|Rac protein signal transduction	endoplasmic reticulum membrane|integral to membrane	GTPase activator activity|lyase activity|protein binding				0																		---	---	---	---
MAP2K1	5604	broad.mit.edu	37	15	66780735	66780735	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66780735delA	uc010bhq.2	+						MAP2K1_uc010ujp.1_Intron	NM_002755	NP_002746			mitogen-activated protein kinase kinase 1						activation of MAPK activity|activation of MAPKK activity|axon guidance|cell cycle arrest|cellular senescence|epidermal growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of cell proliferation|nerve growth factor receptor signaling pathway|Ras protein signal transduction|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|plasma membrane	ATP binding|MAP kinase kinase activity|protein serine/threonine kinase activity|protein tyrosine kinase activity				0														Cardiofaciocutaneous_syndrome				---	---	---	---
RPL4	6124	broad.mit.edu	37	15	66795292	66795292	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66795292delA	uc002apv.2	-						RPL4_uc010bhr.2_Intron|RPL4_uc002apw.2_Intron|RPL4_uc002apx.2_Intron|RPL4_uc010ujq.1_Intron|SNORD18C_uc010bhs.1_5'Flank|SNORD18B_uc002apy.1_5'Flank|SNORD16_uc010bht.2_5'Flank|ZWILCH_uc010bhu.1_5'Flank|ZWILCH_uc002aqb.2_5'Flank|ZWILCH_uc002aqa.2_5'Flank|ZWILCH_uc010bhv.2_5'Flank	NM_000968	NP_000959			ribosomal protein L4						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|nucleolus	protein binding|RNA binding|structural constituent of ribosome				0																		---	---	---	---
AAGAB	79719	broad.mit.edu	37	15	67528577	67528577	+	Intron	DEL	A	-	-	rs35008448		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67528577delA	uc002aqk.3	-						AAGAB_uc002aql.2_Intron|AAGAB_uc010uju.1_Intron	NM_024666	NP_078942			alpha- and gamma-adaptin-binding protein p34						protein transport	cytoplasm					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	68335739	68335740	+	IGR	INS	-	CA	CA	rs150161710	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68335739_68335740insCA								LBXCOR1 (209565 upstream) : PIAS1 (10832 downstream)																																			---	---	---	---
CALML4	91860	broad.mit.edu	37	15	68483097	68483097	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68483097delA	uc002arb.2	-	5					CALML4_uc002arc.2_3'UTR|CALML4_uc002ard.2_RNA|CALML4_uc002are.2_RNA|CALML4_uc010bhz.2_RNA	NM_033429	NP_219501			calmodulin-like 4 isoform 1								calcium ion binding				0																		---	---	---	---
ANP32A	8125	broad.mit.edu	37	15	69072347	69072347	+	3'UTR	DEL	G	-	-	rs3214818		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69072347delG	uc002arl.2	-	7						NM_006305	NP_006296			acidic (leucine-rich) nuclear phosphoprotein 32						intracellular signal transduction|mRNA metabolic process|nucleocytoplasmic transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	endoplasmic reticulum|nucleoplasm|perinuclear region of cytoplasm	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	69888669	69888669	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69888669delT	uc002asi.1	+											Homo sapiens cDNA FLJ40583 fis, clone THYMU2007952.																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	70823725	70823740	+	IGR	DEL	GGAAGGAAGGAGGGAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70823725_70823740delGGAAGGAAGGAGGGAA								TLE3 (433469 upstream) : UACA (123155 downstream)																																			---	---	---	---
UACA	55075	broad.mit.edu	37	15	71005738	71005738	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71005738delA	uc002asr.2	-						UACA_uc010uke.1_Intron	NM_018003	NP_060473			uveal autoantigen with coiled-coil domains and							cytoskeleton|extracellular region				ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
MYO9A	4649	broad.mit.edu	37	15	72252471	72252471	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72252471delA	uc002atl.3	-						MYO9A_uc010biq.2_Intron|MYO9A_uc002ato.2_Intron|MYO9A_uc002atn.1_Intron	NM_006901	NP_008832			myosin IXA						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|visual perception	cytosol|integral to membrane|unconventional myosin complex	actin binding|ATP binding|GTPase activator activity|metal ion binding|motor activity			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
GRAMD2	196996	broad.mit.edu	37	15	72462411	72462411	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72462411delA	uc002atq.2	-						GRAMD2_uc010bis.2_Intron	NM_001012642	NP_001012660			GRAM domain containing 2							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	72531211	72531211	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72531211delT								PKM2 (7527 upstream) : PARP6 (2312 downstream)																																			---	---	---	---
PARP6	56965	broad.mit.edu	37	15	72547519	72547519	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72547519delA	uc002auc.2	-						PARP6_uc002aua.2_Intron|PARP6_uc002aub.2_Intron|PARP6_uc002aud.3_Intron|PARP6_uc002auf.1_Intron	NM_020214	NP_064599			poly (ADP-ribose) polymerase family, member 6								NAD+ ADP-ribosyltransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	72747341	72747341	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72747341delT								TMEM202 (46634 upstream) : ARIH1 (19326 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	72965008	72965008	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72965008delT	uc002auz.1	-						uc010ukt.1_5'Flank|uc010uku.1_5'Flank					DQ594471																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	73265968	73265969	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73265968_73265969delTC								ADPGK (189301 upstream) : NEO1 (78906 downstream)																																			---	---	---	---
NEO1	4756	broad.mit.edu	37	15	73492865	73492866	+	Intron	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73492865_73492866delAG	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																		---	---	---	---
PML	5371	broad.mit.edu	37	15	74324724	74324724	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74324724delA	uc002awv.2	+						PML_uc002awm.2_Intron|PML_uc002awl.2_Intron|PML_uc002awj.1_Intron|PML_uc002awk.2_Intron|PML_uc002awn.2_Intron|PML_uc002awo.2_Intron|PML_uc002awp.2_Intron|PML_uc002awq.2_Intron|PML_uc002awr.2_Intron|PML_uc002aws.2_Intron|PML_uc002awt.2_Intron|PML_uc002awu.2_Intron|PML_uc010ule.1_Intron|PML_uc002awx.2_Intron|PML_uc002awy.2_Intron	NM_033238	NP_150241			promyelocytic leukemia protein isoform 1						cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction resulting in induction of apoptosis|endoplasmic reticulum calcium ion homeostasis|induction of apoptosis|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|maintenance of protein location in nucleus|negative regulation of angiogenesis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of mitotic cell cycle|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|negative regulation of telomerase activity|negative regulation of telomere maintenance via telomerase|negative regulation of transcription, DNA-dependent|negative regulation of translation in response to oxidative stress|PML body organization|PML body organization|positive regulation of defense response to virus by host|positive regulation of histone deacetylation|protein complex assembly|protein stabilization|protein targeting|regulation of calcium ion transport into cytosol|regulation of protein phosphorylation|response to hypoxia|response to virus|transcription, DNA-dependent	cytoplasm|cytosol|early endosome membrane|extrinsic to endoplasmic reticulum membrane|insoluble fraction|nuclear matrix|nuclear membrane|nucleolus|nucleus|PML body	cobalt ion binding|DNA binding|protein binding|protein binding|protein heterodimerization activity|protein homodimerization activity|SUMO binding|transcription coactivator activity|ubiquitin protein ligase binding|zinc ion binding|zinc ion binding			central_nervous_system(2)|kidney(2)|breast(1)	5								T	RARA|PAX5	APL|ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	15	74411558	74411558	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74411558delT								GOLGA6A (36667 upstream) : LOC283731 (7156 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	74993330	74993330	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74993330delT								EDC3 (4944 upstream) : CYP1A1 (18554 downstream)																																			---	---	---	---
SCAMP2	10066	broad.mit.edu	37	15	75158264	75158264	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75158264delC	uc002azb.1	-						SCAMP2_uc010bkg.1_Intron	NM_005697	NP_005688			secretory carrier membrane protein 2						post-Golgi vesicle-mediated transport|protein transport	integral to membrane|nucleus|recycling endosome membrane|trans-Golgi network membrane	protein binding			ovary(1)	1																		---	---	---	---
SCAMP2	10066	broad.mit.edu	37	15	75162764	75162764	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75162764delA	uc002azb.1	-						SCAMP2_uc010bkg.1_Intron	NM_005697	NP_005688			secretory carrier membrane protein 2						post-Golgi vesicle-mediated transport|protein transport	integral to membrane|nucleus|recycling endosome membrane|trans-Golgi network membrane	protein binding			ovary(1)	1																		---	---	---	---
C15orf17	57184	broad.mit.edu	37	15	75200667	75200670	+	5'Flank	DEL	AAAA	-	-	rs150426895		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75200667_75200670delAAAA	uc002azh.3	-						C15orf17_uc010bkh.2_5'Flank|C15orf17_uc002azg.2_5'Flank|C15orf17_uc002azf.2_5'Flank	NM_020447	NP_065180			hypothetical protein LOC57184								cytochrome-c oxidase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	75204581	75204582	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75204581_75204582delTT								C15orf17 (5119 upstream) : COX5A (8037 downstream)																																			---	---	---	---
PTPN9	5780	broad.mit.edu	37	15	75857885	75857885	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75857885delC	uc002bal.2	-							NM_002833	NP_002824			protein tyrosine phosphatase, non-receptor type							cytoplasmic part	non-membrane spanning protein tyrosine phosphatase activity|protein binding			lung(1)|skin(1)	2																		---	---	---	---
PTPN9	5780	broad.mit.edu	37	15	75862369	75862369	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75862369delC	uc002bal.2	-							NM_002833	NP_002824			protein tyrosine phosphatase, non-receptor type							cytoplasmic part	non-membrane spanning protein tyrosine phosphatase activity|protein binding			lung(1)|skin(1)	2																		---	---	---	---
SNUPN	10073	broad.mit.edu	37	15	75891517	75891517	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75891517delA	uc002ban.2	-						SNUPN_uc002bao.2_Intron|SNUPN_uc002bap.2_Intron|SNUPN_uc002baq.2_Intron|SNUPN_uc002bar.2_Intron|SNUPN_uc002bas.2_Intron	NM_005701	NP_005692			snurportin 1						ncRNA metabolic process|protein import into nucleus|spliceosomal snRNP assembly	cytosol|nuclear pore	protein transporter activity|RNA cap binding			pancreas(1)	1																		---	---	---	---
SNUPN	10073	broad.mit.edu	37	15	75904195	75904195	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75904195delA	uc002ban.2	-						SNUPN_uc002bao.2_Intron|SNUPN_uc002bap.2_Intron|SNUPN_uc002baq.2_Intron|SNUPN_uc002bar.2_Intron|SNUPN_uc002bas.2_Intron	NM_005701	NP_005692			snurportin 1						ncRNA metabolic process|protein import into nucleus|spliceosomal snRNP assembly	cytosol|nuclear pore	protein transporter activity|RNA cap binding			pancreas(1)	1																		---	---	---	---
C15orf27	123591	broad.mit.edu	37	15	76374979	76374982	+	Intron	DEL	GAAA	-	-	rs150037882		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76374979_76374982delGAAA	uc002bbq.2	+						C15orf27_uc010bkp.2_Intron	NM_152335	NP_689548			hypothetical protein LOC123591							integral to membrane					0																		---	---	---	---
ETFA	2108	broad.mit.edu	37	15	76577920	76577920	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76577920delA	uc002bbt.2	-						ETFA_uc010bkq.1_Intron|ETFA_uc002bbu.1_Intron	NM_000126	NP_000117			electron transfer flavoprotein, alpha						respiratory electron transport chain|transport	mitochondrial matrix	electron carrier activity|flavin adenine dinucleotide binding|oxidoreductase activity				0																		---	---	---	---
SCAPER	49855	broad.mit.edu	37	15	76965315	76965315	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76965315delA	uc002bby.2	-						SCAPER_uc010bkr.2_Intron|SCAPER_uc002bbx.2_Intron|SCAPER_uc002bbz.1_Intron|SCAPER_uc002bca.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	77094255	77094256	+	Intron	DEL	AA	-	-	rs78364177		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77094255_77094256delAA	uc002bby.2	-						SCAPER_uc002bbx.2_Intron|SCAPER_uc002bbz.1_Intron|SCAPER_uc002bca.1_Intron|SCAPER_uc002bcb.1_Intron|SCAPER_uc002bcc.1_Intron	NM_020843	NP_065894			S-phase cyclin A-associated protein in the ER							endoplasmic reticulum|nucleus	zinc ion binding			large_intestine(1)|lung(1)|ovary(1)	3																		---	---	---	---
SCAPER	49855	broad.mit.edu	37	15	77127609	77127609	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77127609delA	uc002bby.2	-						SCAPER_uc002bbx.2_Intron|SCAPER_uc002bbz.1_Intron|SCAPER_uc002bca.1_Intron|SCAPER_uc002bcb.1_Intron|SCAPER_uc002bcc.1_Intron	NM_020843	NP_065894			S-phase cyclin A-associated protein in the ER							endoplasmic reticulum|nucleus	zinc ion binding			large_intestine(1)|lung(1)|ovary(1)	3																		---	---	---	---
PSTPIP1	9051	broad.mit.edu	37	15	77327921	77327921	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77327921delG	uc002bcf.2	+						PSTPIP1_uc010bkt.1_Intron|PSTPIP1_uc010bku.1_Intron|PSTPIP1_uc002bcg.2_Intron|PSTPIP1_uc010bkw.1_Intron|PSTPIP1_uc002bch.1_Intron|PSTPIP1_uc002bci.1_Intron	NM_003978	NP_003969			proline-serine-threonine phosphatase interacting						cell adhesion|signal transduction	cleavage furrow|lamellipodium|perinuclear region of cytoplasm	catalytic activity			ovary(1)	1																		---	---	---	---
TBC1D2B	23102	broad.mit.edu	37	15	78316385	78316386	+	Intron	DEL	AT	-	-	rs1992470	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78316385_78316386delAT	uc002bcy.3	-						TBC1D2B_uc010bla.2_Intron	NM_144572	NP_653173			TBC1 domain family, member 2B isoform a							intracellular	protein binding|Rab GTPase activator activity			ovary(1)|large_intestine(1)|breast(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	78845698	78845698	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78845698delT								PSMA4 (4138 upstream) : CHRNA5 (12208 downstream)																																			---	---	---	---
MORF4L1	10933	broad.mit.edu	37	15	79171818	79171819	+	Intron	INS	-	C	C	rs143409031	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79171818_79171819insC	uc002bel.2	+						MORF4L1_uc010bli.1_Intron|MORF4L1_uc010blj.1_Intron|MORF4L1_uc002bem.2_Intron|MORF4L1_uc010une.1_Intron	NM_206839	NP_996670			MORF-related gene 15 isoform 2						double-strand break repair via homologous recombination|histone deacetylation|histone H2A acetylation|histone H4 acetylation|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|Sin3 complex	protein N-terminus binding				0																		---	---	---	---
RASGRF1	5923	broad.mit.edu	37	15	79275229	79275229	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79275229delT	uc002beq.2	-						RASGRF1_uc002bep.2_Intron|RASGRF1_uc010blm.1_Intron|RASGRF1_uc002beo.2_Intron	NM_002891	NP_002882			Ras protein-specific guanine						activation of Rac GTPase activity|apoptosis|induction of apoptosis by extracellular signals|long-term memory|nerve growth factor receptor signaling pathway|neuron projection development|regulation of Rac protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|growth cone|plasma membrane|synaptosome	Rho guanyl-nucleotide exchange factor activity			skin(4)|ovary(1)|central_nervous_system(1)	6																		---	---	---	---
RASGRF1	5923	broad.mit.edu	37	15	79377278	79377278	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79377278delT	uc002beq.2	-						RASGRF1_uc002bep.2_Intron|RASGRF1_uc002ber.3_Intron	NM_002891	NP_002882			Ras protein-specific guanine						activation of Rac GTPase activity|apoptosis|induction of apoptosis by extracellular signals|long-term memory|nerve growth factor receptor signaling pathway|neuron projection development|regulation of Rac protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|growth cone|plasma membrane|synaptosome	Rho guanyl-nucleotide exchange factor activity			skin(4)|ovary(1)|central_nervous_system(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	79430860	79430860	+	IGR	DEL	G	-	-	rs869672	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79430860delG								RASGRF1 (47645 upstream) : MIR184 (71270 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	79570321	79570324	+	IGR	DEL	CTTT	-	-	rs60144797		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79570321_79570324delCTTT								MIR184 (68108 upstream) : ANKRD34C (4822 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	79948010	79948010	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79948010delT								KIAA1024 (183368 upstream) : MTHFS (189310 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	80436828	80436829	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80436828_80436829insA								ZFAND6 (6118 upstream) : FAH (8302 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	80522762	80522762	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80522762delT								FAH (44080 upstream) : ARNT2 (173930 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	80542676	80542676	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80542676delT								FAH (63994 upstream) : ARNT2 (154016 downstream)																																			---	---	---	---
FAM108C1	58489	broad.mit.edu	37	15	81043707	81043707	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81043707delA	uc002bfu.2	+						FAM108C1_uc002bft.2_Intron	NM_021214	NP_067037			hypothetical protein LOC58489								hydrolase activity				0																		---	---	---	---
KIAA1199	57214	broad.mit.edu	37	15	81120726	81120727	+	Intron	DEL	AA	-	-	rs113892730		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81120726_81120727delAA	uc002bfw.1	+						KIAA1199_uc010unn.1_Intron	NM_018689	NP_061159			KIAA1199 precursor											upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	81327974	81327974	+	IGR	DEL	T	-	-	rs112120799		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81327974delT								MESDC1 (31630 upstream) : C15orf26 (63775 downstream)																																			---	---	---	---
C15orf26	161502	broad.mit.edu	37	15	81429912	81429912	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81429912delG	uc002bgb.2	+						C15orf26_uc010blp.1_Intron	NM_173528	NP_775799			hypothetical protein LOC161502												0																		---	---	---	---
C15orf26	161502	broad.mit.edu	37	15	81436282	81436282	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81436282delT	uc002bgb.2	+							NM_173528	NP_775799			hypothetical protein LOC161502												0																		---	---	---	---
IL16	3603	broad.mit.edu	37	15	81569371	81569371	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81569371delA	uc002bgh.3	+						IL16_uc002bgc.2_Intron|IL16_uc010blq.1_Intron|IL16_uc002bge.3_Intron|IL16_uc010unp.1_Intron|IL16_uc002bgg.2_Intron|IL16_uc002bgi.1_5'Flank	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	82154212	82154213	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82154212_82154213delAA								TMC3 (487794 upstream) : MEX3B (179915 downstream)																																			---	---	---	---
FSD2	123722	broad.mit.edu	37	15	83438318	83438318	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83438318delA	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	83527427	83527428	+	Intron	DEL	CA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83527427_83527428delCA	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																		---	---	---	---
HOMER2	9455	broad.mit.edu	37	15	83529709	83529710	+	Intron	DEL	GA	-	-	rs71948611		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83529709_83529710delGA	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																		---	---	---	---
ADAMTSL3	57188	broad.mit.edu	37	15	84472895	84472895	+	Intron	DEL	A	-	-	rs143020265		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84472895delA	uc002bjz.3	+						ADAMTSL3_uc002bjy.1_Intron|ADAMTSL3_uc010bmt.1_Intron|ADAMTSL3_uc010bmu.1_Intron	NM_207517	NP_997400			ADAMTS-like 3 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(6)|central_nervous_system(5)|lung(5)|large_intestine(4)|breast(3)|skin(2)|kidney(1)|pancreas(1)	27			BRCA - Breast invasive adenocarcinoma(143;0.211)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	85070267	85070267	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85070267delA								GOLGA6L5 (10189 upstream) : UBE2Q2P1 (160 downstream)																																			---	---	---	---
ZSCAN2	54993	broad.mit.edu	37	15	85160662	85160662	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85160662delA	uc002bkr.2	+						ZSCAN2_uc010bmz.1_Intron|ZSCAN2_uc010bna.2_Intron|ZSCAN2_uc010uox.1_Intron|ZSCAN2_uc010uoy.1_Intron|ZSCAN2_uc010uoz.1_Intron	NM_181877	NP_870992			zinc finger protein 29 isoform 1						cell differentiation|multicellular organismal development|spermatogenesis|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2				UCEC - Uterine corpus endometrioid carcinoma (272;0.168)|all cancers(203;5.43e-22)														---	---	---	---
WDR73	84942	broad.mit.edu	37	15	85190734	85190734	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85190734delT	uc002bkw.2	-						WDR73_uc002bkv.2_Intron|WDR73_uc002bkx.2_Intron|WDR73_uc010upa.1_Intron	NM_032856	NP_116245			WD repeat domain 73												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	85824686	85824687	+	IGR	DEL	CA	-	-	rs34213744		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85824686_85824687delCA								PDE8A (142316 upstream) : AKAP13 (99184 downstream)																																			---	---	---	---
AKAP13	11214	broad.mit.edu	37	15	85998456	85998456	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85998456delT	uc002blv.1	+						AKAP13_uc002bls.2_Intron|AKAP13_uc002blt.1_Intron|AKAP13_uc002blu.1_Intron	NM_007200	NP_009131			A-kinase anchor protein 13 isoform 2						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|liver(1)|skin(1)|ovary(1)	9																		---	---	---	---
AKAP13	11214	broad.mit.edu	37	15	86251033	86251034	+	Intron	DEL	AA	-	-	rs112571964		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86251033_86251034delAA	uc002blv.1	+						AKAP13_uc002blu.1_Intron|AKAP13_uc010bnf.1_Intron|AKAP13_uc002blw.1_Intron|AKAP13_uc002blx.1_Intron	NM_007200	NP_009131			A-kinase anchor protein 13 isoform 2						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|liver(1)|skin(1)|ovary(1)	9																		---	---	---	---
KLHL25	64410	broad.mit.edu	37	15	86333323	86333324	+	Intron	INS	-	TTG	TTG			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86333323_86333324insTTG	uc002bly.2	-							NM_022480	NP_071925			BTB/POZ KELCH domain protein							cytoplasm				ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	88151515	88151515	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88151515delC								NCRNA00052 (28598 upstream) : NTRK3 (268473 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	88340488	88340489	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88340488_88340489insA								NCRNA00052 (217571 upstream) : NTRK3 (79499 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	88383533	88383534	+	IGR	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88383533_88383534delGT								NCRNA00052 (260616 upstream) : NTRK3 (36454 downstream)																																			---	---	---	---
NTRK3	4916	broad.mit.edu	37	15	88670279	88670279	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88670279delT	uc002bme.1	-						NTRK3_uc002bmh.2_Intron|NTRK3_uc002bmf.1_Intron|NTRK3_uc010upl.1_Intron|NTRK3_uc010bnh.1_Intron|NTRK3_uc002bmg.2_Intron	NM_001012338	NP_001012338			neurotrophic tyrosine kinase, receptor, type 3						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity		ETV6/NTRK3(234)	soft_tissue(85)|kidney(66)|breast(56)|salivary_gland(26)|lung(22)|large_intestine(6)|ovary(6)|stomach(5)|central_nervous_system(3)|pancreas(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1)	281			BRCA - Breast invasive adenocarcinoma(143;0.211)					T	ETV6	congenital fibrosarcoma|Secretory breast 					TSP Lung(13;0.10)			---	---	---	---
Unknown	0	broad.mit.edu	37	15	88983624	88983625	+	IGR	DEL	GA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88983624_88983625delGA								NTRK3 (183963 upstream) : MRPL46 (19083 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	89209129	89209130	+	IGR	INS	-	AA	AA			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89209129_89209130insAA								ISG20 (10250 upstream) : ACAN (137544 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	89235454	89235454	+	IGR	DEL	A	-	-	rs78563153		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89235454delA								ISG20 (36575 upstream) : ACAN (111220 downstream)																																			---	---	---	---
ABHD2	11057	broad.mit.edu	37	15	89644099	89644099	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89644099delA	uc002bnj.2	+						ABHD2_uc010ups.1_Intron|ABHD2_uc002bnk.2_Intron	NM_007011	NP_008942			alpha/beta hydrolase domain containing protein							integral to membrane	carboxylesterase activity			ovary(1)|lung(1)	2	Lung NSC(78;0.0472)|all_lung(78;0.089)																	---	---	---	---
ABHD2	11057	broad.mit.edu	37	15	89728843	89728843	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89728843delA	uc002bnj.2	+						ABHD2_uc002bnk.2_Intron	NM_007011	NP_008942			alpha/beta hydrolase domain containing protein							integral to membrane	carboxylesterase activity			ovary(1)|lung(1)	2	Lung NSC(78;0.0472)|all_lung(78;0.089)																	---	---	---	---
TTLL13	440307	broad.mit.edu	37	15	90798089	90798089	+	Intron	DEL	A	-	-	rs113825723		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90798089delA	uc002bpd.1	+						TTLL13_uc002bpe.1_Intron	NM_001029964	NP_001025135			tubulin tyrosine ligase-like family, member 13						protein modification process		ATP binding|tubulin-tyrosine ligase activity				0	Melanoma(11;0.00551)|Lung NSC(78;0.0178)|all_lung(78;0.0378)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|BRCA - Breast invasive adenocarcinoma(143;0.0323)|Kidney(142;0.0514)															---	---	---	---
IQGAP1	8826	broad.mit.edu	37	15	90972029	90972029	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90972029delA	uc002bpl.1	+							NM_003870	NP_003861			IQ motif containing GTPase activating protein 1						energy reserve metabolic process|regulation of insulin secretion|small GTPase mediated signal transduction	actin filament|cytoplasm|midbody|nucleus|plasma membrane	calmodulin binding|GTPase inhibitor activity|protein phosphatase binding|Ras GTPase activator activity			ovary(2)|lung(2)|central_nervous_system(2)|pancreas(1)|skin(1)	8	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)															---	---	---	---
IQGAP1	8826	broad.mit.edu	37	15	90999352	90999352	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90999352delA	uc002bpl.1	+							NM_003870	NP_003861			IQ motif containing GTPase activating protein 1						energy reserve metabolic process|regulation of insulin secretion|small GTPase mediated signal transduction	actin filament|cytoplasm|midbody|nucleus|plasma membrane	calmodulin binding|GTPase inhibitor activity|protein phosphatase binding|Ras GTPase activator activity			ovary(2)|lung(2)|central_nervous_system(2)|pancreas(1)|skin(1)	8	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)															---	---	---	---
UNC45A	55898	broad.mit.edu	37	15	91479413	91479413	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91479413delC	uc002bqg.2	+						UNC45A_uc002bqd.2_Intron|UNC45A_uc010uqo.1_Intron|UNC45A_uc010uqp.1_RNA|UNC45A_uc010uqq.1_Intron	NM_018671	NP_061141			smooth muscle cell associated protein-1 isoform						cell differentiation|muscle organ development	nucleus|perinuclear region of cytoplasm	protein binding			ovary(2)	2	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)															---	---	---	---
SV2B	9899	broad.mit.edu	37	15	91650305	91650306	+	Intron	DEL	TG	-	-	rs148110411	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91650305_91650306delTG	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)															---	---	---	---
SLCO3A1	28232	broad.mit.edu	37	15	92459128	92459128	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92459128delG	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)															---	---	---	---
CHD2	1106	broad.mit.edu	37	15	93471726	93471727	+	Intron	INS	-	ATTT	ATTT	rs141229681	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93471726_93471727insATTT	uc002bsp.2	+						CHD2_uc002bsm.1_Intron|CHD2_uc002bsn.2_Intron|CHD2_uc002bso.1_Intron|CHD2_uc010urb.1_Intron	NM_001271	NP_001262			chromodomain helicase DNA binding protein 2						regulation of transcription from RNA polymerase II promoter	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding			ovary(1)|skin(1)	2	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	93794806	93794806	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93794806delG								RGMA (162373 upstream) : MCTP2 (979995 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	95102798	95102800	+	IGR	DEL	TTG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95102798_95102800delTTG								MCTP2 (75618 upstream) : LOC145820 (873522 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	95211387	95211390	+	IGR	DEL	AGAG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95211387_95211390delAGAG								MCTP2 (184207 upstream) : LOC145820 (764932 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	96174499	96174499	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96174499delT								LOC145820 (123425 upstream) : NR2F2 (694658 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	97182996	97182997	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97182996_97182997delAA								NR2F2 (299506 upstream) : SPATA8 (143682 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	97195018	97195019	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97195018_97195019insA								NR2F2 (311528 upstream) : SPATA8 (131660 downstream)																																			---	---	---	---
IGF1R	3480	broad.mit.edu	37	15	99410384	99410387	+	Intron	DEL	GAGA	-	-	rs113100053		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99410384_99410387delGAGA	uc002bul.2	+						IGF1R_uc010urq.1_Intron|IGF1R_uc010bon.2_Intron	NM_000875	NP_000866			insulin-like growth factor 1 receptor precursor						anti-apoptosis|immune response|insulin receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of DNA replication|protein autophosphorylation|protein tetramerization	microsome	ATP binding|identical protein binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor receptor activity|metal ion binding|phosphatidylinositol 3-kinase binding			lung(3)|kidney(3)|ovary(1)|central_nervous_system(1)	8	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Mecasermin(DB01277)													---	---	---	---
ADAMTS17	170691	broad.mit.edu	37	15	100648377	100648377	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100648377delC	uc002bvv.1	-						ADAMTS17_uc002bvx.1_Intron	NM_139057	NP_620688			ADAM metallopeptidase with thrombospondin type 1						proteolysis	intracellular|proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	101250263	101250265	+	IGR	DEL	TGG	-	-	rs113180907		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101250263_101250265delTGG								ASB7 (58361 upstream) : ALDH1A3 (169744 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	101287963	101287964	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101287963_101287964delTT								ASB7 (96061 upstream) : ALDH1A3 (132045 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	102319213	102319213	+	5'Flank	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102319213delC	uc002cdb.2	+											DQ596816																														---	---	---	---
LUC7L	55692	broad.mit.edu	37	16	271712	271712	+	Intron	DEL	A	-	-	rs12103033	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:271712delA	uc002cgc.1	-						LUC7L_uc002cga.1_Intron|LUC7L_uc002cgd.1_Intron|LUC7L_uc002cge.1_Intron	NM_201412	NP_958815			LUC7-like isoform b								metal ion binding			central_nervous_system(1)	1		all_cancers(16;1.1e-06)|all_epithelial(16;2.71e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.0138)|all_lung(18;0.0306)																---	---	---	---
AXIN1	8312	broad.mit.edu	37	16	337965	337965	+	3'UTR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:337965delC	uc002cgp.1	-	11					AXIN1_uc002cgq.1_3'UTR	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	1076821	1076822	+	IGR	INS	-	T	T	rs148007746	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1076821_1076822insT								SOX8 (39843 upstream) : LOC146336 (37262 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	1296896	1296897	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1296896_1296897delAA								TPSAB1 (4342 upstream) : TPSD1 (9376 downstream)																																			---	---	---	---
IFT140	9742	broad.mit.edu	37	16	1636312	1636312	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1636312delA	uc002cmb.2	-						IFT140_uc002clz.2_5'Flank	NM_014714	NP_055529			intraflagellar transport 140											ovary(3)|pancreas(1)|skin(1)	5		Hepatocellular(780;0.219)																---	---	---	---
HN1L	90861	broad.mit.edu	37	16	1739233	1739234	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1739233_1739234delAA	uc002cmg.2	+						HN1L_uc010uvi.1_Intron|HN1L_uc010brt.2_Intron|HN1L_uc010bru.2_Intron|HN1L_uc010uvj.1_Intron|HN1L_uc010uvk.1_Intron	NM_144570	NP_653171			hematological and neurological expressed 1-like							cytoplasm|nucleus				upper_aerodigestive_tract(1)	1																		---	---	---	---
FAHD1	81889	broad.mit.edu	37	16	1882763	1882767	+	Intron	DEL	CTCTC	-	-	rs4017981		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1882763_1882767delCTCTC	uc002cnd.2	+						FAHD1_uc010brz.2_Intron	NM_001018104	NP_001018114			fumarylacetoacetate hydrolase domain containing							mitochondrion	hydrolase activity|metal ion binding|protein binding				0																		---	---	---	---
ABCA3	21	broad.mit.edu	37	16	2358198	2358198	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2358198delG	uc002cpy.1	-						ABCA3_uc010bsk.1_Intron|ABCA3_uc010bsl.1_Intron	NM_001089	NP_001080			ATP-binding cassette, sub-family A member 3						response to drug	integral to membrane|lamellar body|membrane fraction|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			breast(5)|ovary(5)|central_nervous_system(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	16		Ovarian(90;0.17)																---	---	---	---
PRSS27	83886	broad.mit.edu	37	16	2763103	2763103	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2763103delT	uc002crf.2	-						PRSS27_uc002cre.2_Intron|PRSS27_uc002crg.2_Intron|PRSS27_uc010bst.1_3'UTR	NM_031948	NP_114154			marapsin precursor						proteolysis	extracellular region	serine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
CCDC64B	146439	broad.mit.edu	37	16	3084713	3084714	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3084713_3084714delTT	uc002ctf.3	-						CCDC64B_uc002cte.3_5'Flank	NM_001103175	NP_001096645			coiled-coil domain containing 64B												0																		---	---	---	---
BTBD12	84464	broad.mit.edu	37	16	3656253	3656254	+	Intron	INS	-	A	A	rs79957697		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3656253_3656254insA	uc002cvp.2	-						BTBD12_uc002cvq.1_Intron	NM_032444	NP_115820			BTB (POZ) domain containing 12						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	3858158	3858158	+	Intron	DEL	G	-	-	rs74003411	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3858158delG	uc002cvv.2	-						CREBBP_uc002cvw.2_Intron	NM_004380	NP_004371			CREB binding protein isoform a						cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia	cytoplasm|nuclear body	histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1)	127		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)				T|N|F|Mis|O	MLL|MORF|RUNXBP2	ALL|AML|DLBCL|B-NHL 		Rubinstein-Taybi syndrome		Rubinstein-Taybi_syndrome				---	---	---	---
SRL	6345	broad.mit.edu	37	16	4286652	4286652	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4286652delT	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	4407345	4407348	+	Intron	DEL	TTTC	-	-	rs71402532		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4407345_4407348delTTTC	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																		---	---	---	---
MGRN1	23295	broad.mit.edu	37	16	4710994	4710994	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4710994delT	uc002cwz.2	+						MGRN1_uc002cxa.2_Intron|MGRN1_uc010btx.2_Intron|MGRN1_uc010btw.2_Intron|MGRN1_uc002cxb.2_Intron|MGRN1_uc010uxo.1_Intron|MGRN1_uc010uxp.1_Intron|MGRN1_uc010uxq.1_Intron	NM_001142290	NP_001135762			mahogunin, ring finger 1 isoform 3						endosome to lysosome transport|negative regulation of cAMP-mediated signaling|negative regulation of G-protein coupled receptor protein signaling pathway|protein monoubiquitination	cytosol|early endosome|nucleus|plasma membrane|plasma membrane	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
NUDT16L1	84309	broad.mit.edu	37	16	4744734	4744734	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4744734delG	uc002cxe.2	+						NUDT16L1_uc002cxf.1_3'UTR	NM_032349	NP_115725			syndesmos							cytoplasm	hydrolase activity				0																		---	---	---	---
PPL	5493	broad.mit.edu	37	16	4952586	4952586	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4952586delG	uc002cyd.1	-							NM_002705	NP_002696			periplakin						keratinization	cytoskeleton|desmosome|mitochondrion|nucleus	protein binding|structural constituent of cytoskeleton			ovary(4)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	5302840	5302840	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5302840delC	uc002cyq.1	+											Homo sapiens cDNA clone IMAGE:5244947, **** WARNING: chimeric clone ****.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	5555080	5555080	+	Intron	DEL	T	-	-	rs71404526		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5555080delT	uc002cyq.1	+											Homo sapiens cDNA clone IMAGE:5244947, **** WARNING: chimeric clone ****.																														---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	6391230	6391230	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6391230delT	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron	NM_018723	NP_061193			ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)														---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	6743093	6743095	+	Intron	DEL	CAT	-	-	rs117535707		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6743093_6743095delCAT	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	6922563	6922563	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6922563delA	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	6940521	6940524	+	Intron	DEL	AAAC	-	-	rs142779350		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6940521_6940524delAAAC	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	7013289	7013290	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7013289_7013290delTT	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	7111573	7111573	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7111573delA	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron|A2BP1_uc010uyb.1_Intron	NM_018723	NP_061193			ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	8105774	8105776	+	IGR	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8105774_8105776delAAA								A2BP1 (342434 upstream) : TMEM114 (513727 downstream)																																			---	---	---	---
C16orf68	79091	broad.mit.edu	37	16	8733741	8733742	+	Intron	INS	-	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8733741_8733742insC	uc002cyz.2	+						C16orf68_uc002cza.2_Intron	NM_024109	NP_077014			hypothetical protein LOC79091								methyltransferase activity				0																		---	---	---	---
ABAT	18	broad.mit.edu	37	16	8793841	8793841	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8793841delT	uc002czc.3	+							NM_020686	NP_065737			4-aminobutyrate aminotransferase precursor						behavioral response to cocaine|gamma-aminobutyric acid catabolic process|neurotransmitter catabolic process|neurotransmitter secretion	4-aminobutyrate transaminase complex|mitochondrial matrix	(S)-3-amino-2-methylpropionate transaminase activity|4-aminobutyrate transaminase activity|protein homodimerization activity|pyridoxal phosphate binding|succinate-semialdehyde dehydrogenase binding			upper_aerodigestive_tract(1)	1					Divalproex sodium(DB00510)|Isoniazid(DB00951)|L-Alanine(DB00160)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)|Pyruvic acid(DB00119)|Tiagabine(DB00906)|Valproic Acid(DB00313)|Vigabatrin(DB01080)													---	---	---	---
ABAT	18	broad.mit.edu	37	16	8855047	8855047	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8855047delC	uc002czc.3	+						ABAT_uc002czd.3_Intron|ABAT_uc010buh.2_Intron|ABAT_uc010bui.2_Intron	NM_020686	NP_065737			4-aminobutyrate aminotransferase precursor						behavioral response to cocaine|gamma-aminobutyric acid catabolic process|neurotransmitter catabolic process|neurotransmitter secretion	4-aminobutyrate transaminase complex|mitochondrial matrix	(S)-3-amino-2-methylpropionate transaminase activity|4-aminobutyrate transaminase activity|protein homodimerization activity|pyridoxal phosphate binding|succinate-semialdehyde dehydrogenase binding			upper_aerodigestive_tract(1)	1					Divalproex sodium(DB00510)|Isoniazid(DB00951)|L-Alanine(DB00160)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)|Pyruvic acid(DB00119)|Tiagabine(DB00906)|Valproic Acid(DB00313)|Vigabatrin(DB01080)													---	---	---	---
USP7	7874	broad.mit.edu	37	16	9014408	9014408	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9014408delT	uc002czl.2	-						USP7_uc010uyk.1_Intron|USP7_uc010uyj.1_Intron|USP7_uc002czk.2_Intron|USP7_uc010uyl.1_Intron	NM_003470	NP_003461			ubiquitin specific peptidase 7						interspecies interaction between organisms|multicellular organismal development|protein deubiquitination|regulation of sequence-specific DNA binding transcription factor activity|ubiquitin-dependent protein catabolic process	cytoplasm|PML body	cysteine-type endopeptidase activity|p53 binding|protein C-terminus binding|transcription factor binding|ubiquitin protein ligase binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)	3																		---	---	---	---
USP7	7874	broad.mit.edu	37	16	9042825	9042825	+	Intron	DEL	A	-	-	rs112677679		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9042825delA	uc002czl.2	-						USP7_uc010uyk.1_Intron|USP7_uc010uyl.1_Intron	NM_003470	NP_003461			ubiquitin specific peptidase 7						interspecies interaction between organisms|multicellular organismal development|protein deubiquitination|regulation of sequence-specific DNA binding transcription factor activity|ubiquitin-dependent protein catabolic process	cytoplasm|PML body	cysteine-type endopeptidase activity|p53 binding|protein C-terminus binding|transcription factor binding|ubiquitin protein ligase binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	9132319	9132319	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9132319delA								USP7 (74978 upstream) : C16orf72 (53218 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	9493489	9493489	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9493489delA								C16orf72 (279944 upstream) : GRIN2A (353778 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	10446651	10446651	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10446651delA								GRIN2A (170040 upstream) : ATF7IP2 (33261 downstream)																																			---	---	---	---
ATF7IP2	80063	broad.mit.edu	37	16	10532277	10532280	+	Intron	DEL	TTTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10532277_10532280delTTTT	uc002czu.2	+						ATF7IP2_uc002czv.2_Intron|ATF7IP2_uc010uyo.1_Intron|ATF7IP2_uc010uyp.1_Intron|ATF7IP2_uc002czw.2_Intron|ATF7IP2_uc010uyq.1_Intron	NM_024997	NP_079273			activating transcription factor 7 interacting						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0																		---	---	---	---
FAM18A	780776	broad.mit.edu	37	16	10868933	10868933	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10868933delA	uc010buo.1	-	3	381	c.110delT	c.(109-111)TTCfs	p.F37fs	FAM18A_uc010uyr.1_Intron|FAM18A_uc010uys.1_Intron|FAM18A_uc010uyt.1_RNA|FAM18A_uc010bun.2_RNA|FAM18A_uc010uyu.1_Intron|FAM18A_uc002dad.3_RNA|FAM18A_uc002daf.1_RNA|FAM18A_uc002dae.1_5'UTR	NM_001079512	NP_001072980	A6NH52	FA18A_HUMAN	hypothetical protein LOC780776	37	Helical; (Potential).					integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	10961780	10961780	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10961780delT								FAM18A (49159 upstream) : CIITA (9275 downstream)																																			---	---	---	---
CIITA	4261	broad.mit.edu	37	16	10981354	10981354	+	Intron	DEL	T	-	-	rs35292035		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10981354delT	uc002dai.3	+						CIITA_uc002daj.3_Intron|CIITA_uc002dak.3_Intron|CIITA_uc002dag.2_Intron|CIITA_uc002dah.2_Intron|CIITA_uc010bup.1_Intron	NM_000246	NP_000237			class II transactivator						interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|response to antibiotic|transcription, DNA-dependent	nucleus	activating transcription factor binding|ATP binding|protein C-terminus binding|protein complex binding|transcription coactivator activity|transcription regulatory region DNA binding			central_nervous_system(1)	1								T	FLJ27352|CD274|CD273|RALGDS|RUNDC2A|C16orf75	PMBL|Hodgkin Lymphona|								---	---	---	---
Unknown	0	broad.mit.edu	37	16	11584728	11584728	+	Intron	DEL	G	-	-	rs79336876	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11584728delG	uc002dax.1	-											Homo sapiens cDNA FLJ44575 fis, clone UTERU3018154.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	12031882	12031883	+	IGR	DEL	TG	-	-	rs116770375		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12031882_12031883delTG								GSPT1 (21363 upstream) : TNFRSF17 (27081 downstream)																																			---	---	---	---
CPPED1	55313	broad.mit.edu	37	16	12895311	12895311	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12895311delA	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	12982211	12982213	+	IGR	DEL	TTT	-	-	rs58850170		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12982211_12982213delTTT								CPPED1 (84467 upstream) : SHISA9 (13264 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	13946742	13946742	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13946742delA								SHISA9 (612470 upstream) : ERCC4 (67272 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	14126875	14126875	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14126875delT								ERCC4 (80670 upstream) : MKL2 (38321 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	14520182	14520182	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14520182delA								MIR365-1 (116954 upstream) : PARN (9377 downstream)																																			---	---	---	---
PARN	5073	broad.mit.edu	37	16	14668033	14668033	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14668033delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	15379571	15379572	+	IGR	INS	-	A	A	rs3045394	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15379571_15379572insA								PDXDC1 (146376 upstream) : MPV17L (110039 downstream)																																			---	---	---	---
C16orf45	89927	broad.mit.edu	37	16	15587593	15587594	+	Intron	INS	-	C	C	rs147261586	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15587593_15587594insC	uc002ddo.2	+							NM_033201	NP_149978			hypothetical protein LOC89927 isoform 1											ovary(1)	1																		---	---	---	---
C16orf45	89927	broad.mit.edu	37	16	15643814	15643814	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15643814delT	uc002ddo.2	+						C16orf45_uc002ddp.2_Intron	NM_033201	NP_149978			hypothetical protein LOC89927 isoform 1											ovary(1)	1																		---	---	---	---
NDE1	54820	broad.mit.edu	37	16	15758917	15758917	+	Intron	DEL	T	-	-	rs79093814		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15758917delT	uc002ddt.1	+						NDE1_uc010uzy.1_Intron|NDE1_uc002dds.2_Intron	NM_017668	NP_060138			nuclear distribution gene E homolog 1						cell differentiation|cell division|centrosome duplication|establishment of chromosome localization|establishment of mitotic spindle orientation|G2/M transition of mitotic cell cycle|mitotic prometaphase|nervous system development	cleavage furrow|condensed chromosome kinetochore|cytosol|microtubule|spindle pole centrosome	microtubule binding			ovary(1)	1																		---	---	---	---
MYH11	4629	broad.mit.edu	37	16	15840927	15840928	+	Intron	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15840927_15840928delAG	uc002ddy.2	-						MYH11_uc002ddv.2_Intron|MYH11_uc002ddw.2_Intron|MYH11_uc002ddx.2_Intron|MYH11_uc010bvg.2_Intron	NM_002474	NP_002465			smooth muscle myosin heavy chain 11 isoform						axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction	cytosol|melanosome|muscle myosin complex|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(6)|skin(3)|lung(2)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)	15								T	CBFB	AML								---	---	---	---
ABCC1	4363	broad.mit.edu	37	16	16079833	16079833	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16079833delT	uc010bvi.2	+						ABCC1_uc010bvj.2_Intron|ABCC1_uc010bvk.2_Intron|ABCC1_uc010bvl.2_Intron|ABCC1_uc010bvm.2_Intron	NM_004996	NP_004987			ATP-binding cassette, sub-family C, member 1						hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process|response to drug	Golgi apparatus|integral to plasma membrane|membrane fraction|nucleus	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)	4					Daunorubicin(DB00694)|Glibenclamide(DB01016)|Probenecid(DB01032)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)													---	---	---	---
ABCC1	4363	broad.mit.edu	37	16	16103895	16103905	+	Intron	DEL	TTTTTTTTTTT	-	-	rs71388789		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16103895_16103905delTTTTTTTTTTT	uc010bvi.2	+						ABCC1_uc010bvj.2_Intron|ABCC1_uc010bvk.2_Intron|ABCC1_uc010bvl.2_Intron|ABCC1_uc010bvm.2_Intron|ABCC1_uc002del.3_Intron	NM_004996	NP_004987			ATP-binding cassette, sub-family C, member 1						hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process|response to drug	Golgi apparatus|integral to plasma membrane|membrane fraction|nucleus	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)	4					Daunorubicin(DB00694)|Glibenclamide(DB01016)|Probenecid(DB01032)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	17035679	17035680	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17035679_17035680insT								LOC339047 (591242 upstream) : XYLT1 (160503 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	17806148	17806148	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17806148delA								XYLT1 (241410 upstream) : NOMO2 (705035 downstream)																																			---	---	---	---
SMG1	23049	broad.mit.edu	37	16	18844064	18844064	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18844064delT	uc002dfm.2	-						SMG1_uc010bwb.2_Intron|SMG1_uc010bwa.2_Intron	NM_015092	NP_055907			PI-3-kinase-related kinase SMG-1						DNA repair|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|peptidyl-serine phosphorylation|phosphatidylinositol phosphorylation|protein autophosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			breast(5)|stomach(4)|lung(4)|kidney(2)|ovary(1)	16																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	19388025	19388026	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19388025_19388026delAA								LOC728276 (72309 upstream) : TMC5 (33835 downstream)																																			---	---	---	---
TMC5	79838	broad.mit.edu	37	16	19443726	19443727	+	Intron	INS	-	AAAC	AAAC	rs34596434		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19443726_19443727insAAAC	uc002dgc.3	+						TMC5_uc010vaq.1_Intron|TMC5_uc002dgb.3_Intron|TMC5_uc010var.1_Intron	NM_001105248	NP_001098718			transmembrane channel-like 5 isoform a							integral to membrane				skin(1)	1																		---	---	---	---
C16orf62	57020	broad.mit.edu	37	16	19670010	19670011	+	Intron	DEL	AA	-	-	rs67938972		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19670010_19670011delAA	uc002dgn.1	+						C16orf62_uc002dgo.1_Intron|C16orf62_uc002dgp.1_Intron	NM_020314	NP_064710			hypothetical protein LOC57020							integral to membrane				ovary(1)	1																		---	---	---	---
C16orf88	400506	broad.mit.edu	37	16	19718989	19718989	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19718989delC	uc002dgq.2	-							NM_001012991	NP_001013009			hypothetical protein LOC400506							nucleolus					0																		---	---	---	---
IQCK	124152	broad.mit.edu	37	16	19751137	19751137	+	Intron	DEL	A	-	-	rs72152898		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19751137delA	uc002dgr.2	+						IQCK_uc002dgs.2_Intron|IQCK_uc010vat.1_Intron|IQCK_uc010bwc.2_Intron|IQCK_uc010vau.1_Intron	NM_153208	NP_694940			IQ motif containing K											skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	20195682	20195693	+	IGR	DEL	TGTGTGTGTGTG	-	-	rs67779358		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20195682_20195693delTGTGTGTGTGTG								GPR139 (110582 upstream) : GP2 (126119 downstream)																																			---	---	---	---
ACSM5	54988	broad.mit.edu	37	16	20429352	20429352	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20429352delT	uc002dhe.2	+						ACSM5_uc002dhd.1_Intron	NM_017888	NP_060358			acyl-CoA synthetase medium-chain family member 5						fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|GTP binding|metal ion binding			ovary(2)	2																		---	---	---	---
DNAH3	55567	broad.mit.edu	37	16	20948487	20948487	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20948487delT	uc010vbe.1	-						DNAH3_uc010vbd.1_Intron	NM_017539	NP_060009			dynein, axonemal, heavy chain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)														---	---	---	---
DNAH3	55567	broad.mit.edu	37	16	21082669	21082669	+	Intron	DEL	T	-	-	rs35116457		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21082669delT	uc010vbe.1	-							NM_017539	NP_060009			dynein, axonemal, heavy chain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	21197794	21197794	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21197794delA								TMEM159 (5859 upstream) : ZP2 (10979 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	21587687	21587687	+	Intron	DEL	A	-	-	rs71374879		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21587687delA	uc002diq.3	+											Homo sapiens cDNA FLJ59829 complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	21890632	21890632	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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																														---	---	---	---
EEF2K	29904	broad.mit.edu	37	16	22293529	22293529	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22293529delA	uc002dki.2	+						EEF2K_uc002dkh.2_Intron	NM_013302	NP_037434			elongation factor-2 kinase						insulin receptor signaling pathway|translational elongation	cytosol	ATP binding|calcium ion binding|calmodulin binding|elongation factor-2 kinase activity|translation factor activity, nucleic acid binding			large_intestine(1)	1				GBM - Glioblastoma multiforme(48;0.0223)														---	---	---	---
CDR2	1039	broad.mit.edu	37	16	22359259	22359259	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22359259delT	uc002dkn.2	-							NM_001802	NP_001793			cerebellar degeneration-related protein 2							nucleus	protein binding			skin(1)	1				GBM - Glioblastoma multiforme(48;0.0188)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	22430070	22430070	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22430070delA								CDR2 (44132 upstream) : RRN3P3 (797 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	22704734	22704734	+	IGR	DEL	T	-	-	rs35749100		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22704734delT								LOC653786 (116548 upstream) : HS3ST2 (121126 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	22708660	22708660	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22708660delT								LOC653786 (120474 upstream) : HS3ST2 (117200 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	23069340	23069340	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23069340delA								HS3ST2 (141683 upstream) : USP31 (3389 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	23790955	23790956	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23790955_23790956delAA								CHP2 (20699 upstream) : PRKCB (56344 downstream)																																			---	---	---	---
PRKCB	5579	broad.mit.edu	37	16	24072389	24072389	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24072389delT	uc002dmd.2	+						PRKCB_uc002dme.2_Intron	NM_212535	NP_997700			protein kinase C, beta isoform 1						apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)													---	---	---	---
PRKCB	5579	broad.mit.edu	37	16	24124749	24124749	+	Intron	DEL	C	-	-	rs111953721	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24124749delC	uc002dmd.2	+						PRKCB_uc002dme.2_Intron	NM_212535	NP_997700			protein kinase C, beta isoform 1						apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)													---	---	---	---
PRKCB	5579	broad.mit.edu	37	16	24225934	24225934	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24225934delT	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)													---	---	---	---
TNRC6A	27327	broad.mit.edu	37	16	24813291	24813292	+	Intron	DEL	AG	-	-	rs72165127		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24813291_24813292delAG	uc002dmm.2	+						TNRC6A_uc010bxs.2_Intron|TNRC6A_uc002dmn.2_Intron|TNRC6A_uc002dmo.2_Intron|TNRC6A_uc002dmp.2_5'Flank|TNRC6A_uc002dmq.2_5'Flank	NM_014494	NP_055309			trinucleotide repeat containing 6A						negative regulation of translation involved in gene silencing by miRNA	cytoplasmic mRNA processing body|micro-ribonucleoprotein complex	nucleotide binding|RNA binding			ovary(2)	2				GBM - Glioblastoma multiforme(48;0.0394)														---	---	---	---
HS3ST4	9951	broad.mit.edu	37	16	26043748	26043748	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26043748delA	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	26385831	26385831	+	IGR	DEL	G	-	-	rs72532698		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26385831delG								HS3ST4 (236823 upstream) : C16orf82 (692388 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	26412460	26412460	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26412460delT								HS3ST4 (263452 upstream) : C16orf82 (665759 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	26855912	26855915	+	IGR	DEL	AAAA	-	-	rs78929028		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26855912_26855915delAAAA								HS3ST4 (706904 upstream) : C16orf82 (222304 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	26907690	26907691	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26907690_26907691delAC								HS3ST4 (758682 upstream) : C16orf82 (170528 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	27320614	27320615	+	IGR	INS	-	G	G	rs149281196	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27320614_27320615insG								NSMCE1 (40501 upstream) : IL4R (4636 downstream)																																			---	---	---	---
GTF3C1	2975	broad.mit.edu	37	16	27543194	27543195	+	Intron	DEL	GA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27543194_27543195delGA	uc002dov.1	-						GTF3C1_uc002dou.2_Intron	NM_001520	NP_001511			general transcription factor IIIC, polypeptide							transcription factor TFIIIC complex	DNA binding|protein binding			ovary(2)|pancreas(1)|breast(1)|skin(1)	5																		---	---	---	---
GSG1L	146395	broad.mit.edu	37	16	27882800	27882800	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27882800delA	uc002doz.2	-						GSG1L_uc010bya.1_Intron|GSG1L_uc010bxz.1_Intron|GSG1L_uc002doy.2_Intron	NM_001109763	NP_001103233			GSG1-like isoform 1							integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	28254990	28254991	+	IGR	INS	-	TGTG	TGTG	rs141362891	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28254990_28254991insTGTG								XPO6 (31800 upstream) : SBK1 (48849 downstream)																																			---	---	---	---
SBK1	388228	broad.mit.edu	37	16	28324919	28324922	+	Intron	DEL	AAAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28324919_28324922delAAAA	uc002dpd.2	+							NM_001024401	NP_001019572			SH3-binding kinase 1							cytoplasm	ATP binding|protein serine/threonine kinase activity			ovary(1)|kidney(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	28531699	28531699	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28531699delA	uc010vct.1	-											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	28959758	28959759	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28959758_28959759delTT	uc010vct.1	-						NFATC2IP_uc002drt.2_5'Flank|NFATC2IP_uc002dru.2_5'Flank|NFATC2IP_uc010vdg.1_5'Flank					RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																														---	---	---	---
BOLA2	552900	broad.mit.edu	37	16	29565652	29565652	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29565652delG	uc010bzb.1	-						LOC440354_uc002dsp.3_Intron|uc002dtf.2_Intron|LOC440354_uc010bza.1_Intron|LOC440354_uc002dtj.2_Intron|LOC440354_uc010vds.1_Intron					SubName: Full=Putative uncharacterized protein ENSP00000369970; Flags: Fragment;												0																		---	---	---	---
QPRT	23475	broad.mit.edu	37	16	29694679	29694679	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29694679delT	uc002dto.2	+						uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|QPRT_uc010vdu.1_Intron	NM_014298	NP_055113			quinolinate phosphoribosyltransferase						protein oligomerization|quinolinate catabolic process|water-soluble vitamin metabolic process	cytosol	nicotinate-nucleotide diphosphorylase (carboxylating) activity|protein homodimerization activity				0					Niacin(DB00627)													---	---	---	---
BOLA2	552900	broad.mit.edu	37	16	30183416	30183416	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30183416delA	uc010bzb.1	-						uc002dtf.2_Intron					SubName: Full=Putative uncharacterized protein ENSP00000369970; Flags: Fragment;												0																		---	---	---	---
LOC595101	595101	broad.mit.edu	37	16	30326505	30326505	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30326505delA	uc002dxp.1	-							NR_002453				Homo sapiens cDNA FLJ39663 fis, clone SMINT2007187.												0																		---	---	---	---
SRCAP	10847	broad.mit.edu	37	16	30751142	30751143	+	3'UTR	INS	-	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30751142_30751143insG	uc002dze.1	+	34					SRCAP_uc002dzf.2_RNA|SRCAP_uc002dzg.1_3'UTR	NM_006662	NP_006653			Snf2-related CBP activator protein						interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|nucleus|protein complex	ATP binding|DNA binding|helicase activity|histone acetyltransferase activity|transcription coactivator activity			ovary(3)|skin(1)	4			Colorectal(24;0.198)															---	---	---	---
SETD1A	9739	broad.mit.edu	37	16	30988278	30988278	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30988278delT	uc002ead.1	+							NM_014712	NP_055527			SET domain containing 1A						regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nuclear speck|Set1C/COMPASS complex	histone-lysine N-methyltransferase activity|nucleotide binding|protein binding|RNA binding			ovary(2)|skin(1)	3																		---	---	---	---
STX4	6810	broad.mit.edu	37	16	31046367	31046367	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31046367delT	uc002eal.2	+						STX4_uc002eak.2_Intron|STX4_uc002eam.2_Intron	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																		---	---	---	---
STX4	6810	broad.mit.edu	37	16	31050769	31050769	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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																		---	---	---	---
PRSS53	339105	broad.mit.edu	37	16	31106653	31106653	+	5'Flank	DEL	A	-	-	rs74635928		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31106653delA	uc002ear.2	-						VKORC1_uc002eas.2_5'Flank|VKORC1_uc002eat.2_5'Flank|VKORC1_uc002eau.2_5'Flank	NM_001039503	NP_001034592			polyserase 3 precursor						proteolysis	extracellular region	serine-type endopeptidase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	31248388	31248388	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31248388delT								TRIM72 (11878 upstream) : ITGAM (22900 downstream)																																			---	---	---	---
ITGAM	3684	broad.mit.edu	37	16	31287662	31287662	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31287662delT	uc002ebq.2	+						ITGAM_uc002ebr.2_Intron|ITGAM_uc010cam.1_Intron	NM_000632	NP_000623			integrin alpha M isoform 2 precursor						blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration	integrin complex	glycoprotein binding|receptor activity			kidney(1)	1																		---	---	---	---
C16orf58	64755	broad.mit.edu	37	16	31509422	31509424	+	Intron	DEL	GAG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31509422_31509424delGAG	uc002eci.1	-						C16orf58_uc010vfq.1_Intron	NM_022744	NP_073581			hypothetical protein LOC64755							integral to membrane				ovary(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	32177847	32177850	+	IGR	DEL	TTGA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32177847_32177850delTTGA								HERC2P4 (13973 upstream) : TP53TG3B (506991 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32282850	32282850	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32282850delA								HERC2P4 (118976 upstream) : TP53TG3B (401991 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32528674	32528675	+	IGR	INS	-	CATA	CATA	rs56779030	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32528674_32528675insCATA								HERC2P4 (364800 upstream) : TP53TG3B (156166 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32574917	32574918	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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	32596625	32596625	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32596625delT								HERC2P4 (432751 upstream) : TP53TG3B (88216 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32611985	32611985	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32611985delT								HERC2P4 (448111 upstream) : TP53TG3B (72856 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32636143	32636143	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32636143delA								HERC2P4 (472269 upstream) : TP53TG3B (48698 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32657837	32657839	+	IGR	DEL	CAC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32657837_32657839delCAC								HERC2P4 (493963 upstream) : TP53TG3B (27002 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32819123	32819125	+	IGR	DEL	TCA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32819123_32819125delTCA								TP53TG3B (130245 upstream) : SLC6A10P (69672 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32833097	32833097	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32833097delA								TP53TG3B (144219 upstream) : SLC6A10P (55700 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33380654	33380655	+	IGR	INS	-	G	G	rs143152195		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33380654_33380655insG								SLC6A10P (484191 upstream) : MIR1826 (584853 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33387797	33387798	+	IGR	INS	-	C	C	rs71158810		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33387797_33387798insC								SLC6A10P (491334 upstream) : MIR1826 (577710 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33441507	33441507	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33441507delA								SLC6A10P (545044 upstream) : MIR1826 (524001 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33706231	33706231	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33706231delT								SLC6A10P (809768 upstream) : MIR1826 (259277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33857420	33857421	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33857420_33857421insA								SLC6A10P (960957 upstream) : MIR1826 (108087 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33957978	33957979	+	IGR	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33957978_33957979delCT								None (None upstream) : MIR1826 (7529 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	34179236	34179236	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34179236delC								MIR1826 (213644 upstream) : UBE2MP1 (224566 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	34678481	34678481	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34678481delA								LOC283914 (52397 upstream) : LOC146481 (33304 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	34858418	34858418	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34858418delC								LOC146481 (143451 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	35010688	35010688	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:35010688delT								LOC146481 (295721 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	35269702	35269702	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:35269702delA								LOC146481 (554735 upstream) : None (None downstream)																																			---	---	---	---
SHCBP1	79801	broad.mit.edu	37	16	46625513	46625513	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46625513delA	uc002eec.3	-							NM_024745	NP_079021			SHC SH2-domain binding protein 1											ovary(1)|breast(1)	2		all_cancers(37;0.00404)|all_epithelial(9;0.00527)|all_lung(18;0.0413)|Lung NSC(13;0.213)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	46876402	46876404	+	IGR	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46876402_46876404delAAA								C16orf87 (11328 upstream) : GPT2 (41904 downstream)																																			---	---	---	---
ITFG1	81533	broad.mit.edu	37	16	47326466	47326466	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47326466delT	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	48095651	48095651	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48095651delT								PHKB (360218 upstream) : ABCC12 (21233 downstream)																																			---	---	---	---
ABCC12	94160	broad.mit.edu	37	16	48151850	48151850	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48151850delG	uc002efc.1	-						ABCC12_uc002eey.1_Intron|ABCC12_uc002eez.1_Intron|ABCC12_uc002efa.1_Intron|ABCC12_uc002efb.1_Intron|ABCC12_uc002efd.1_Intron	NM_033226	NP_150229			ATP-binding cassette protein C12							integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3		all_cancers(37;0.0474)|all_lung(18;0.047)														OREG0023771	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SIAH1	6477	broad.mit.edu	37	16	48459176	48459176	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48459176delA	uc002efl.2	-											Homo sapiens SIAH1 mRNA for seven in absentia homolog 1 isoform a, complete cds, clone: FLJ08065AAAN.						axon guidance|cell cycle|neuron apoptosis|proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|spermatogenesis	beta-catenin destruction complex|cytosol|nucleus	protein C-terminus binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		all_cancers(37;0.157)|all_lung(18;0.11)|Breast(268;0.238)																---	---	---	---
SIAH1	6477	broad.mit.edu	37	16	48475745	48475745	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48475745delG	uc002efl.2	-											Homo sapiens SIAH1 mRNA for seven in absentia homolog 1 isoform a, complete cds, clone: FLJ08065AAAN.						axon guidance|cell cycle|neuron apoptosis|proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|spermatogenesis	beta-catenin destruction complex|cytosol|nucleus	protein C-terminus binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		all_cancers(37;0.157)|all_lung(18;0.11)|Breast(268;0.238)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	48743292	48743292	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48743292delT								N4BP1 (99172 upstream) : CBLN1 (568919 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	49083178	49083178	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49083178delA								N4BP1 (439058 upstream) : CBLN1 (229033 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	49246505	49246505	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49246505delA								N4BP1 (602385 upstream) : CBLN1 (65706 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	49376258	49376259	+	IGR	INS	-	C	C	rs143803459	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49376258_49376259insC								CBLN1 (60543 upstream) : C16orf78 (31549 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	49448841	49448842	+	IGR	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49448841_49448842delGT								C16orf78 (15524 upstream) : ZNF423 (75680 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	50080933	50080936	+	IGR	DEL	AAAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50080933_50080936delAAAA								TMEM188 (9935 upstream) : HEATR3 (18945 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	50440001	50440001	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50440001delA								BRD7 (37172 upstream) : NKD1 (142240 downstream)																																			---	---	---	---
CYLD	1540	broad.mit.edu	37	16	50827271	50827271	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50827271delA	uc002egp.1	+						CYLD_uc010cbs.1_Intron|CYLD_uc002egq.1_Intron|CYLD_uc002egr.1_Intron	NM_015247	NP_056062			ubiquitin carboxyl-terminal hydrolase CYLD						cell cycle|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|protein K63-linked deubiquitination|regulation of microtubule cytoskeleton organization|regulation of mitotic cell cycle|translation|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway	cytosol|extrinsic to internal side of plasma membrane|microtubule|perinuclear region of cytoplasm|ribosome	proline-rich region binding|protein kinase binding|structural constituent of ribosome|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			skin(19)|large_intestine(3)|haematopoietic_and_lymphoid_tissue(3)|central_nervous_system(3)	28		all_cancers(37;0.0156)						Mis|N|F|S		cylindroma	cylindroma			Familial_Cylindromatosis|Multiple_Trichoepithelioma_Familial				---	---	---	---
Unknown	0	broad.mit.edu	37	16	51411491	51411492	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51411491_51411492insA								SALL1 (226308 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	51529545	51529545	+	IGR	DEL	T	-	-	rs72185695		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51529545delT								SALL1 (344362 upstream) : TOX3 (942373 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	51617765	51617765	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51617765delT								SALL1 (432582 upstream) : TOX3 (854153 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	51624301	51624302	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51624301_51624302insT								SALL1 (439118 upstream) : TOX3 (847616 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	51999448	51999449	+	IGR	DEL	AC	-	-	rs151050939		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51999448_51999449delAC								SALL1 (814265 upstream) : TOX3 (472469 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	52380534	52380534	+	IGR	DEL	A	-	-	rs35796167		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52380534delA								None (None upstream) : TOX3 (91384 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	52755262	52755264	+	IGR	DEL	TTT	-	-	rs113350700		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52755262_52755264delTTT								TOX3 (173548 upstream) : CHD9 (333681 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	52878848	52878849	+	IGR	INS	-	TGTG	TGTG	rs11642732		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52878848_52878849insTGTG								TOX3 (297134 upstream) : CHD9 (210096 downstream)																																			---	---	---	---
CHD9	80205	broad.mit.edu	37	16	53348724	53348724	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53348724delT	uc002ehb.2	+						CHD9_uc002egy.2_Intron|CHD9_uc002ehc.2_Intron|CHD9_uc002ehf.2_Intron|CHD9_uc010cbw.2_Intron	NM_025134	NP_079410			chromodomain helicase DNA binding protein 9						cellular lipid metabolic process|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleoplasm	ATP binding|DNA binding|helicase activity|protein binding			lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1)	7		all_cancers(37;0.0212)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	53368579	53368579	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53368579delA								CHD9 (7166 upstream) : RBL2 (99772 downstream)																																			---	---	---	---
RBL2	5934	broad.mit.edu	37	16	53515565	53515565	+	Intron	DEL	T	-	-	rs72027669		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53515565delT	uc002ehi.3	+						RBL2_uc002ehj.2_Intron|RBL2_uc010vgw.1_Intron	NM_005611	NP_005602			retinoblastoma-like 2 (p130)						cell cycle|chromatin modification|regulation of cell cycle|regulation of lipid kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding			ovary(2)|lung(2)|upper_aerodigestive_tract(1)	5																		---	---	---	---
FTO	79068	broad.mit.edu	37	16	53965784	53965785	+	Intron	DEL	AC	-	-	rs35135177		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53965784_53965785delAC	uc002ehr.2	+						FTO_uc010vha.1_Intron|FTO_uc010cbz.2_Intron|FTO_uc002ehs.2_5'Flank	NM_001080432	NP_001073901			fat mass and obesity associated						DNA dealkylation involved in DNA repair|oxidative single-stranded DNA demethylation|oxidative single-stranded RNA demethylation|RNA repair	nucleus	DNA-N1-methyladenine dioxygenase activity|ferrous iron binding|oxidative DNA demethylase activity|oxidative RNA demethylase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	54706263	54706263	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54706263delA								IRX3 (385885 upstream) : IRX5 (258848 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	54935112	54935112	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54935112delT								IRX3 (614734 upstream) : IRX5 (29999 downstream)																																			---	---	---	---
IRX5	10265	broad.mit.edu	37	16	54967956	54967956	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54967956delA	uc002ehv.2	+	3					IRX5_uc002ehw.2_3'UTR	NM_005853	NP_005844			iroquois homeobox protein 5						response to stimulus|visual perception	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|vitamin D binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	55316924	55316925	+	IGR	DEL	TT	-	-	rs72293419		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55316924_55316925delTT								IRX5 (348531 upstream) : IRX6 (41546 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	55681326	55681333	+	IGR	DEL	GGAGGGAA	-	-	rs116579043	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55681326_55681333delGGAGGGAA								LPCAT2 (60745 upstream) : SLC6A2 (8689 downstream)																																			---	---	---	---
SLC6A2	6530	broad.mit.edu	37	16	55730393	55730393	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55730393delA	uc002eif.2	+						SLC6A2_uc010ccd.2_Intron|SLC6A2_uc002eig.2_Intron|SLC6A2_uc002eih.2_Intron|SLC6A2_uc002eii.2_Intron|SLC6A2_uc002eij.2_Intron	NM_001043	NP_001034			solute carrier family 6 member 2						synaptic transmission	integral to plasma membrane|membrane fraction	norepinephrine:sodium symporter activity			lung(4)|ovary(2)|pancreas(2)	8				BRCA - Breast invasive adenocarcinoma(181;0.01)|Kidney(780;0.0267)	Amineptine(DB04836)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Atomoxetine(DB00289)|Bethanidine(DB00217)|Bupropion(DB01156)|Clomipramine(DB01242)|Cocaine(DB00907)|Debrisoquin(DB04840)|Desipramine(DB01151)|Diethylpropion(DB00937)|Doxepin(DB01142)|Duloxetine(DB00476)|Ergotamine(DB00696)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Imipramine(DB00458)|Maprotiline(DB00934)|Mazindol(DB00579)|Methylphenidate(DB00422)|Milnacipran(DB04896)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Paroxetine(DB00715)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Protriptyline(DB00344)|Reboxetine(DB00234)|Sibutramine(DB01105)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Venlafaxine(DB00285)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	55963853	55963853	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55963853delA								CES7 (4481 upstream) : LOC283856 (163046 downstream)																																			---	---	---	---
BBS2	583	broad.mit.edu	37	16	56532619	56532619	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56532619delA	uc002ejd.2	-						BBS2_uc010ccg.2_3'UTR	NM_031885	NP_114091			Bardet-Biedl syndrome 2 protein						adult behavior|brain morphogenesis|cerebral cortex development|cilium morphogenesis|fat cell differentiation|hippocampus development|melanosome transport|negative regulation of multicellular organism growth|photoreceptor cell maintenance|protein localization to organelle|regulation of cilium beat frequency involved in ciliary motility|sperm axoneme assembly|striatum development	BBSome|cilium membrane|microtubule basal body|motile cilium	protein binding			ovary(1)	1														Bardet-Biedl_syndrome				---	---	---	---
SLC12A3	6559	broad.mit.edu	37	16	56901339	56901339	+	Intron	DEL	G	-	-	rs150940148	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56901339delG	uc010ccm.2	+						SLC12A3_uc002ekd.3_Intron|SLC12A3_uc010ccn.2_Intron	NM_001126108	NP_001119580			solute carrier family 12, member 3 isoform 3						sodium ion transmembrane transport	apical plasma membrane|integral to plasma membrane|membrane fraction	sodium:chloride symporter activity			ovary(2)|breast(1)	3					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)											OREG0011897|OREG0023817	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)|type=TRANSCRIPTION FACTOR BINDING SITE|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip); Conservation found by scanning with a motif model	---	---	---	---
FAM192A	80011	broad.mit.edu	37	16	57206385	57206385	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57206385delA	uc010vhk.1	-						FAM192A_uc002ekz.3_Intron|FAM192A_uc002ekv.3_Intron|FAM192A_uc002ekw.3_Intron|FAM192A_uc002ekx.3_Intron|FAM192A_uc002eky.3_Intron|FAM192A_uc010ccx.2_Intron	NM_024946	NP_079222			NEFA-interacting nuclear protein NIP30							nucleus					0																		---	---	---	---
CCL17	6361	broad.mit.edu	37	16	57441658	57441660	+	Intron	DEL	CAT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57441658_57441660delCAT	uc002elj.1	+						CCL17_uc010ccz.1_Intron	NM_002987	NP_002978			small inducible cytokine A17 precursor						cell-cell signaling|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|inflammatory response|multicellular organismal development	extracellular space	chemokine activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	57699074	57699075	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57699074_57699075delAA								GPR56 (130 upstream) : GPR97 (3082 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	58246775	58246776	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58246775_58246776delAA								CSNK2A2 (14993 upstream) : CCDC113 (37064 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	58958433	58958436	+	IGR	DEL	ATGT	-	-	rs72071142		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58958433_58958436delATGT								GOT2 (190187 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	59504805	59504806	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59504805_59504806insT								GOT2 (736559 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	59635449	59635449	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59635449delT								GOT2 (867203 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	59788032	59788034	+	IGR	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59788032_59788034delTTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	60510392	60510392	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60510392delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	60582599	60582600	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60582599_60582600delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	60781433	60781433	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60781433delA								None (None upstream) : CDH8 (905802 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	62445056	62445056	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62445056delT								CDH8 (375020 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	62874809	62874809	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62874809delT								CDH8 (804773 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	64293621	64293621	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64293621delA								None (None upstream) : CDH11 (687064 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	64591910	64591910	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64591910delT								None (None upstream) : CDH11 (388775 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	66037725	66037725	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66037725delA								LOC283867 (427522 upstream) : CDH5 (362800 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	66270228	66270228	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66270228delT								LOC283867 (660025 upstream) : CDH5 (130297 downstream)																																			---	---	---	---
BEAN	146227	broad.mit.edu	37	16	66487246	66487247	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66487246_66487247delAC	uc002eoq.2	+						BEAN_uc002eop.1_Intron	NM_001136106	NP_001129578			brain expressed, associated with Nedd4						cell death	integral to membrane					0																		---	---	---	---
CMTM3	123920	broad.mit.edu	37	16	66636385	66636385	+	5'Flank	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66636385delA	uc002epu.2	+						CMTM3_uc002epv.2_5'Flank|CMTM3_uc002epw.2_5'Flank|CMTM3_uc002epx.2_5'Flank|CMTM3_uc002epy.2_5'Flank	NM_001048251	NP_001041716			chemokine-like factor superfamily 3						chemotaxis	extracellular space|integral to membrane	cytokine activity			central_nervous_system(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0671)|Epithelial(162;0.164)														---	---	---	---
CMTM4	146223	broad.mit.edu	37	16	66651271	66651271	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66651271delA	uc002epz.2	-						CMTM4_uc002eqa.2_3'UTR	NM_178818	NP_848933			chemokine-like factor superfamily 4 isoform 1						chemotaxis	extracellular space|integral to membrane	cytokine activity			pancreas(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0811)|Epithelial(162;0.214)														---	---	---	---
CMTM4	146223	broad.mit.edu	37	16	66693278	66693279	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66693278_66693279delAA	uc002epz.2	-						CMTM4_uc002eqa.2_Intron	NM_178818	NP_848933			chemokine-like factor superfamily 4 isoform 1						chemotaxis	extracellular space|integral to membrane	cytokine activity			pancreas(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0811)|Epithelial(162;0.214)														---	---	---	---
CCDC79	283847	broad.mit.edu	37	16	66795675	66795676	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66795675_66795676insA	uc010viv.1	-						CCDC79_uc002eqc.1_Intron	NM_001136505	NP_001129977			coiled-coil domain containing 79						regulation of transcription, DNA-dependent		DNA binding				0																		---	---	---	---
CBFB	865	broad.mit.edu	37	16	67093880	67093881	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67093880_67093881delTT	uc002era.2	+						CBFB_uc002erb.2_Intron|CBFB_uc010vja.1_Intron	NM_001755	NP_001746			core-binding factor, beta subunit isoform 2						transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			breast(2)	2		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00189)|Epithelial(162;0.00755)|all cancers(182;0.066)				T	MYH11	AML								---	---	---	---
AGRP	181	broad.mit.edu	37	16	67520424	67520424	+	5'Flank	DEL	A	-	-	rs76855375		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67520424delA	uc002etg.1	-							NM_001138	NP_001129			agouti related protein homolog isoform 1						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)														---	---	---	---
NUTF2	10204	broad.mit.edu	37	16	67890091	67890091	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67890091delT	uc002eup.2	+						NUTF2_uc010vkf.1_Intron	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)														---	---	---	---
DUS2L	54920	broad.mit.edu	37	16	68101225	68101226	+	Intron	DEL	CC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68101225_68101226delCC	uc002evi.2	+						DUS2L_uc002evj.2_Intron|DUS2L_uc010vkk.1_Intron|DUS2L_uc010cez.2_Intron	NM_017803	NP_060273			dihydrouridine synthase 2-like, SMM1 homolog						tRNA processing	endoplasmic reticulum	double-stranded RNA binding|flavin adenine dinucleotide binding|tRNA dihydrouridine synthase activity				0		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0131)|Epithelial(162;0.0564)														---	---	---	---
NFATC3	4775	broad.mit.edu	37	16	68178420	68178420	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68178420delT	uc002evo.1	+						NFATC3_uc010vkl.1_Intron|NFATC3_uc010vkm.1_Intron|NFATC3_uc010vkn.1_Intron|NFATC3_uc010vko.1_Intron|NFATC3_uc010vkp.1_Intron|NFATC3_uc010vkq.1_Intron|NFATC3_uc002evl.2_Intron|NFATC3_uc002evk.2_Intron|NFATC3_uc002evm.1_Intron|NFATC3_uc002evn.1_Intron|NFATC3_uc010vkr.1_Intron|NFATC3_uc010vks.1_Intron|NFATC3_uc010vkt.1_Intron|NFATC3_uc010vku.1_Intron|NFATC3_uc010vkv.1_Intron|NFATC3_uc010vkw.1_Intron|NFATC3_uc010vkx.1_Intron|NFATC3_uc010vky.1_Intron|NFATC3_uc010vkz.1_Intron|NFATC3_uc010vla.1_Intron|NFATC3_uc010vlb.1_Intron|NFATC3_uc010vlc.1_Intron	NM_173165	NP_775188			nuclear factor of activated T-cells,						inflammatory response|transcription from RNA polymerase II promoter	nucleolus|plasma membrane	DNA binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	3		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	68657894	68657894	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68657894delA								ZFP90 (56856 upstream) : CDH3 (20257 downstream)														p.?(1)																					---	---	---	---
CDH1	999	broad.mit.edu	37	16	68800636	68800637	+	Intron	INS	-	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68800636_68800637insC	uc002ewg.1	+						CDH1_uc010vlj.1_Intron|CDH1_uc010cfg.1_Intron	NM_004360	NP_004351			cadherin 1, type 1 preproprotein						adherens junction organization|cellular component disassembly involved in apoptosis|cellular response to indole-3-methanol|cellular response to lithium ion|homophilic cell adhesion|negative regulation of cell-cell adhesion|positive regulation of transcription factor import into nucleus|positive regulation of transcription, DNA-dependent|regulation of immune response	actin cytoskeleton|aggresome|apical junction complex|catenin complex|cell-cell adherens junction|endosome|focal adhesion|Golgi apparatus|integral to membrane|internal side of plasma membrane|lateral plasma membrane|perinuclear region of cytoplasm	cell adhesion molecule binding|gamma-catenin binding	p.?(1)		breast(148)|stomach(71)|biliary_tract(8)|endometrium(3)|soft_tissue(2)|large_intestine(2)|urinary_tract(2)|oesophagus(2)|ovary(2)|thyroid(1)|central_nervous_system(1)|lung(1)	243		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)				Mis|N|F|S		lobular breast|gastric	gastric			Hereditary_Diffuse_Gastric_Cancer				---	---	---	---
TMCO7	79613	broad.mit.edu	37	16	68952818	68952818	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68952818delA	uc002ewi.3	+							NM_024562	NP_078838			transmembrane and coiled-coil domains 7							integral to membrane	binding				0		Ovarian(137;0.0568)		OV - Ovarian serous cystadenocarcinoma(108;0.0446)|Epithelial(162;0.198)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	69216097	69216097	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69216097delT								CIRH1A (13161 upstream) : SNTB2 (4953 downstream)																																			---	---	---	---
VPS4A	27183	broad.mit.edu	37	16	69358477	69358477	+	3'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69358477delT	uc002eww.2	+	11						NM_013245	NP_037377			vacuolar protein sorting factor 4A						cell cycle|cellular membrane organization|cytokinesis|endosome transport|protein transport	cytosol|late endosome membrane|midbody|perinuclear region of cytoplasm	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein domain specific binding				0		Ovarian(137;0.101)																---	---	---	---
NFAT5	10725	broad.mit.edu	37	16	69710992	69710992	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69710992delT	uc002exm.1	+						NFAT5_uc002exh.1_Intron|NFAT5_uc002exi.2_Intron|NFAT5_uc002exj.1_Intron|NFAT5_uc002exk.1_Intron|NFAT5_uc002exl.1_Intron|NFAT5_uc002exn.1_Intron	NM_006599	NP_006590			nuclear factor of activated T-cells 5 isoform c						excretion|signal transduction|transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	69775288	69775288	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69775288delA								NQO1 (14755 upstream) : NOB1 (487 downstream)																																			---	---	---	---
WWP2	11060	broad.mit.edu	37	16	69807089	69807089	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69807089delT	uc002exu.1	+						WWP2_uc002ext.2_Intron|WWP2_uc002exv.1_Intron	NM_007014	NP_008945			WW domain containing E3 ubiquitin protein ligase						entry of virus into host cell|negative regulation of protein transport|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transporter activity|proteasomal ubiquitin-dependent protein catabolic process|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|ubiquitin ligase complex	RNA polymerase II transcription factor binding|ubiquitin-protein ligase activity			lung(3)|ovary(1)|breast(1)|skin(1)	6																		---	---	---	---
WWP2	11060	broad.mit.edu	37	16	69922613	69922615	+	Intron	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69922613_69922615delTTT	uc002exu.1	+						WWP2_uc002ext.2_Intron|WWP2_uc002exv.1_Intron|WWP2_uc010vlm.1_Intron	NM_007014	NP_008945			WW domain containing E3 ubiquitin protein ligase						entry of virus into host cell|negative regulation of protein transport|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transporter activity|proteasomal ubiquitin-dependent protein catabolic process|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|ubiquitin ligase complex	RNA polymerase II transcription factor binding|ubiquitin-protein ligase activity			lung(3)|ovary(1)|breast(1)|skin(1)	6																		---	---	---	---
WWP2	11060	broad.mit.edu	37	16	69927979	69927982	+	Intron	DEL	TTTT	-	-	rs113980202		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69927979_69927982delTTTT	uc002exu.1	+						WWP2_uc002ext.2_Intron|WWP2_uc002exv.1_Intron|WWP2_uc010vlm.1_Intron	NM_007014	NP_008945			WW domain containing E3 ubiquitin protein ligase						entry of virus into host cell|negative regulation of protein transport|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transporter activity|proteasomal ubiquitin-dependent protein catabolic process|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|ubiquitin ligase complex	RNA polymerase II transcription factor binding|ubiquitin-protein ligase activity			lung(3)|ovary(1)|breast(1)|skin(1)	6																		---	---	---	---
AARS	16	broad.mit.edu	37	16	70303887	70303887	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70303887delT	uc002eyn.1	-						AARS_uc010vlu.1_Intron	NM_001605	NP_001596			alanyl-tRNA synthetase						alanyl-tRNA aminoacylation|tRNA processing	cytosol|soluble fraction	alanine-tRNA ligase activity|ATP binding|metal ion binding|tRNA binding			pancreas(1)	1		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)	L-Alanine(DB00160)													---	---	---	---
AARS	16	broad.mit.edu	37	16	70306036	70306037	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70306036_70306037delAA	uc002eyn.1	-						AARS_uc010vlu.1_5'Flank	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)													---	---	---	---
DDX19A	55308	broad.mit.edu	37	16	70390266	70390266	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70390266delT	uc002eyv.2	+						DDX19B_uc010vly.1_Intron|DDX19A_uc002eys.2_Intron|DDX19A_uc010cfq.1_Intron|DDX19A_uc010cfr.2_Intron|DDX19A_uc010cfs.2_Intron|DDX19A_uc010vlz.1_Intron|DDX19A_uc010vma.1_5'Flank	NM_018332	NP_060802			DDX19-like protein						mRNA transport|protein transport|transmembrane transport	cytoplasm|nuclear membrane|nuclear pore	ATP binding|ATP-dependent helicase activity|RNA binding				0		Ovarian(137;0.221)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	70631128	70631128	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70631128delT								SF3B3 (19558 upstream) : IL34 (49340 downstream)																																			---	---	---	---
HYDIN	54768	broad.mit.edu	37	16	70858436	70858436	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70858436delT	uc002ezr.2	-						HYDIN_uc010cfy.2_Intron	NM_032821	NP_116210			hydrocephalus inducing isoform a											ovary(1)|skin(1)	2		Ovarian(137;0.0654)																---	---	---	---
AP1G1	164	broad.mit.edu	37	16	71783499	71783499	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71783499delT	uc010cgg.2	-						AP1G1_uc002fba.2_Intron|AP1G1_uc002fbb.2_Intron|AP1G1_uc002faz.2_5'Flank	NM_001128	NP_001119			adaptor-related protein complex 1, gamma 1						endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	clathrin adaptor complex|clathrin coated vesicle membrane|cytosol|Golgi membrane|lysosomal membrane|recycling endosome	kinesin binding|protein transporter activity			ovary(2)	2		Ovarian(137;0.125)																---	---	---	---
KIAA0174	9798	broad.mit.edu	37	16	71941858	71941858	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71941858delT	uc002fbj.1	+						KIAA0174_uc010cgh.1_Intron|KIAA0174_uc002fbk.1_Intron|KIAA0174_uc002fbm.1_Intron|KIAA0174_uc002fbl.1_Intron|KIAA0174_uc002fbn.1_Intron|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																		---	---	---	---
ZFHX3	463	broad.mit.edu	37	16	72824341	72824341	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72824341delA	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)																---	---	---	---
ZFHX3	463	broad.mit.edu	37	16	73066225	73066225	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73066225delA	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	73106575	73106576	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73106575_73106576insA								ZFHX3 (13338 upstream) : HTA (19672 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	73106800	73106800	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73106800delT								ZFHX3 (13563 upstream) : HTA (19448 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	73594142	73594143	+	IGR	INS	-	AGTTTATT	AGTTTATT	rs150816421	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73594142_73594143insAGTTTATT								HTA (466472 upstream) : PSMD7 (736538 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	73955123	73955123	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73955123delA								HTA (827453 upstream) : PSMD7 (375558 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	74267012	74267015	+	IGR	DEL	ACAC	-	-	rs71944990		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74267012_74267015delACAC								None (None upstream) : PSMD7 (63666 downstream)																																			---	---	---	---
RFWD3	55159	broad.mit.edu	37	16	74666289	74666290	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74666289_74666290insA	uc002fda.2	-						RFWD3_uc010vmx.1_Intron|RFWD3_uc010cgq.2_Intron	NM_018124	NP_060594			ring finger and WD repeat domain 3						DNA repair|mitotic cell cycle G1/S transition DNA damage checkpoint|response to ionizing radiation	nucleus	MDM2 binding|p53 binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)|breast(1)	3																		---	---	---	---
MLKL	197259	broad.mit.edu	37	16	74721580	74721580	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74721580delT	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																		---	---	---	---
CFDP1	10428	broad.mit.edu	37	16	75402587	75402587	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75402587delT	uc002fdy.2	-						CFDP1_uc002fdz.2_Intron	NM_006324	NP_006315			craniofacial development protein 1						multicellular organismal development					upper_aerodigestive_tract(1)	1																		---	---	---	---
CHST6	4166	broad.mit.edu	37	16	75515917	75515918	+	Intron	INS	-	TAT	TAT	rs143648196	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75515917_75515918insTAT	uc002fef.2	-						CHST6_uc002feg.1_Intron|CHST6_uc002feh.1_Intron	NM_021615	NP_067628			carbohydrate (N-acetylglucosamine 6-O)						keratan sulfate biosynthetic process|N-acetylglucosamine metabolic process	Golgi membrane|integral to membrane	N-acetylglucosamine 6-O-sulfotransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	75560087	75560088	+	IGR	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75560087_75560088delGT								CHST6 (31161 upstream) : CHST5 (2342 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	76079952	76079953	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76079952_76079953delAC								TERF2IP (388624 upstream) : CNTNAP4 (231223 downstream)																																			---	---	---	---
CNTNAP4	85445	broad.mit.edu	37	16	76582685	76582685	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76582685delT	uc002feu.1	+						CNTNAP4_uc002fev.1_Intron|CNTNAP4_uc010chb.1_Intron|CNTNAP4_uc002fex.1_Intron	NM_033401	NP_207837			cell recognition protein CASPR4 isoform 1						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	76880343	76880344	+	IGR	DEL	CA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76880343_76880344delCA								CNTNAP4 (287208 upstream) : MON1B (344492 downstream)																																			---	---	---	---
MON1B	22879	broad.mit.edu	37	16	77230833	77230833	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77230833delG	uc002fez.2	+						MON1B_uc010vnf.1_Intron|MON1B_uc010vng.1_Intron|MON1B_uc002ffa.2_Intron|SYCE1L_uc010vnh.1_5'Flank	NM_014940	NP_055755			MON1 homolog B								protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	77255238	77255238	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77255238delA								SYCE1L (8262 upstream) : ADAMTS18 (60788 downstream)																																			---	---	---	---
WWOX	51741	broad.mit.edu	37	16	78510972	78510972	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78510972delG	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)												OREG0004181|OREG0002521	type=REGULATORY REGION|EvidenceSubtype=In-vivo GFP Expression Assay|type=REGULATORY REGION|Gene=WWOX(intragenic)|Dataset=Vista Enhancers|EvidenceSubtype=In-vivo LacZ Expression Assay	---	---	---	---
WWOX	51741	broad.mit.edu	37	16	78688535	78688536	+	Intron	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78688535_78688536delTC	uc002ffk.2	+						WWOX_uc010vnk.1_Intron|WWOX_uc002ffl.2_Intron|WWOX_uc010che.2_Intron	NM_016373	NP_057457			WW domain-containing oxidoreductase isoform 1						apoptosis|negative regulation of Wnt receptor signaling pathway|steroid metabolic process|Wnt receptor signaling pathway	Golgi apparatus|mitochondrion|nucleus	coenzyme binding|oxidoreductase activity|protein dimerization activity				0		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)														---	---	---	---
WWOX	51741	broad.mit.edu	37	16	78889284	78889285	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78889284_78889285insA	uc002ffk.2	+						WWOX_uc010vnk.1_Intron|WWOX_uc002ffl.2_Intron|WWOX_uc010che.2_Intron	NM_016373	NP_057457			WW domain-containing oxidoreductase isoform 1						apoptosis|negative regulation of Wnt receptor signaling pathway|steroid metabolic process|Wnt receptor signaling pathway	Golgi apparatus|mitochondrion|nucleus	coenzyme binding|oxidoreductase activity|protein dimerization activity				0		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)														---	---	---	---
WWOX	51741	broad.mit.edu	37	16	78914830	78914830	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78914830delT	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	79335317	79335317	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79335317delT								WWOX (88754 upstream) : MAF (292429 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	79390080	79390081	+	IGR	DEL	CA	-	-	rs72800596		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79390080_79390081delCA								WWOX (143517 upstream) : MAF (237665 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	80049975	80049975	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80049975delT								MAF (415353 upstream) : DYNLRB2 (524879 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	80397206	80397207	+	IGR	DEL	GA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80397206_80397207delGA								MAF (762584 upstream) : DYNLRB2 (177647 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	80914895	80914896	+	Intron	DEL	GA	-	-	rs142391838	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80914895_80914896delGA	uc002fft.1	-											Homo sapiens cDNA FLJ35683 fis, clone SPLEN2019131.																														---	---	---	---
CMIP	80790	broad.mit.edu	37	16	81629641	81629641	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81629641delT	uc002fgp.2	+						CMIP_uc002fgq.1_Intron	NM_198390	NP_938204			c-Maf-inducing protein isoform C-mip							cytoplasm|nucleus					0																		---	---	---	---
CMIP	80790	broad.mit.edu	37	16	81671633	81671633	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81671633delC	uc002fgp.2	+						CMIP_uc002fgq.1_Intron|CMIP_uc010vnq.1_Intron	NM_198390	NP_938204			c-Maf-inducing protein isoform C-mip							cytoplasm|nucleus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	81773599	81773600	+	Intron	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81773599_81773600delTG	uc002fgs.2	+											Homo sapiens cDNA clone IMAGE:5787216, partial cds.																														---	---	---	---
CDH13	1012	broad.mit.edu	37	16	83512844	83512844	+	Intron	DEL	G	-	-	rs34218928		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83512844delG	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	83835503	83835503	+	IGR	DEL	A	-	-	rs146705871		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83835503delA								CDH13 (5306 upstream) : HSBP1 (6090 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	83952318	83952318	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83952318delA								MLYCD (2533 upstream) : OSGIN1 (30354 downstream)																																			---	---	---	---
MBTPS1	8720	broad.mit.edu	37	16	84125560	84125560	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84125560delT	uc002fhi.2	-							NM_003791	NP_003782			membrane-bound transcription factor site-1						cholesterol metabolic process|proteolysis	endoplasmic reticulum lumen|endoplasmic reticulum membrane|Golgi membrane|integral to membrane	serine-type endopeptidase activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	85591176	85591176	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85591176delT								FAM92B (445062 upstream) : KIAA0182 (53853 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	86837919	86837920	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86837919_86837920delAA								FOXL1 (222616 upstream) : FBXO31 (525024 downstream)																																			---	---	---	---
ZCCHC14	23174	broad.mit.edu	37	16	87463221	87463221	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87463221delT	uc002fjz.1	-						ZCCHC14_uc002fka.1_Intron	NM_015144	NP_055959			zinc finger, CCHC domain containing 14						cell communication		nucleic acid binding|phosphatidylinositol binding|zinc ion binding			upper_aerodigestive_tract(1)|breast(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0285)														---	---	---	---
BANP	54971	broad.mit.edu	37	16	88038970	88038970	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88038970delT	uc002fkr.2	+						BANP_uc002fkp.2_Intron|BANP_uc002fkq.2_Intron|BANP_uc010vow.1_Intron|BANP_uc002fks.3_Intron|BANP_uc002fko.1_Intron|BANP_uc010vov.1_Intron	NM_079837	NP_524576			BTG3 associated nuclear protein isoform b						cell cycle|chromatin modification|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0				BRCA - Breast invasive adenocarcinoma(80;0.00551)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	88195321	88195321	+	IGR	DEL	A	-	-	rs7201322	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88195321delA								BANP (84398 upstream) : ZNF469 (298558 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	88447330	88447335	+	IGR	DEL	ACACAG	-	-	rs118144537		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88447330_88447335delACACAG								BANP (336407 upstream) : ZNF469 (46544 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	88626493	88626493	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88626493delA	uc010vox.1	-											RecName: Full=Putative uncharacterized protein C16orf85;																														---	---	---	---
FAM38A	9780	broad.mit.edu	37	16	88823176	88823176	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88823176delA	uc010vpb.1	-							NM_001142864	NP_001136336			family with sequence similarity 38, member A							endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|integral to membrane|plasma membrane	ion channel activity				0																		---	---	---	---
FAM38A	9780	broad.mit.edu	37	16	88848520	88848520	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88848520delT	uc010vpb.1	-							NM_001142864	NP_001136336			family with sequence similarity 38, member A							endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|integral to membrane|plasma membrane	ion channel activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	89060043	89060043	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89060043delC								CBFA2T3 (16642 upstream) : ACSF3 (100211 downstream)																																			---	---	---	---
RPL13	6137	broad.mit.edu	37	16	89624291	89624293	+	5'Flank	DEL	CTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89624291_89624293delCTT	uc002fnm.1	+						RPL13_uc010vpj.1_5'Flank|RPL13_uc002fnn.1_5'Flank	NM_000977	NP_000968			ribosomal protein L13						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic ribosome	protein binding|RNA binding|structural constituent of ribosome				0		all_hematologic(23;0.0748)		all cancers(4;1.15e-07)|OV - Ovarian serous cystadenocarcinoma(4;7.8e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0139)												OREG0024053	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
DPEP1	1800	broad.mit.edu	37	16	89701269	89701269	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89701269delT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	89888200	89888201	+	IGR	DEL	TG	-	-	rs142887608		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89888200_89888201delTG								FANCA (5135 upstream) : SPIRE2 (6706 downstream)																																			---	---	---	---
LOC100130015	100130015	broad.mit.edu	37	16	90113019	90113020	+	Intron	INS	-	CAGTGA	CAGTGA	rs145225004	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90113019_90113020insCAGTGA	uc010cjd.2	-						LOC100130015_uc002fql.2_Intron	NR_027336				SubName: Full=cDNA FLJ52651; SubName: Full=Putative uncharacterized protein ENSP00000387338;												0																		---	---	---	---
VPS53	55275	broad.mit.edu	37	17	533039	533039	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:533039delA	uc002frn.2	-						VPS53_uc002frk.2_Intron|VPS53_uc010cjo.1_Intron|VPS53_uc002frl.2_Intron|VPS53_uc002frm.2_Intron|VPS53_uc002fro.2_Intron|VPS53_uc010cjp.1_Intron	NM_018289	NP_060759			vacuolar protein sorting 53 isoform 2						protein transport	endosome membrane|Golgi apparatus					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	1218752	1218752	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1218752delA								TUSC5 (14471 upstream) : YWHAE (29084 downstream)																																			---	---	---	---
YWHAE	7531	broad.mit.edu	37	17	1290793	1290793	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1290793delA	uc002fsj.2	-						YWHAE_uc002fsk.2_Intron|YWHAE_uc010vqh.1_Intron|YWHAE_uc010vqi.1_Intron	NM_006761	NP_006752			tyrosine 3/tryptophan 5 -monooxygenase						apoptosis|G2/M transition of mitotic cell cycle|induction of apoptosis by extracellular signals|interspecies interaction between organisms|intracellular signal transduction|nerve growth factor receptor signaling pathway	cytosol|melanosome	histone deacetylase binding|phosphoserine binding			lung(2)|ovary(1)	3			OV - Ovarian serous cystadenocarcinoma(18;0.203)	UCEC - Uterine corpus endometrioid carcinoma (25;0.0887)														---	---	---	---
RTN4RL1	146760	broad.mit.edu	37	17	1866238	1866238	+	Intron	DEL	T	-	-	rs71375577		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1866238delT	uc002ftp.2	-							NM_178568	NP_848663			reticulon 4 receptor-like 1 precursor						axon regeneration	anchored to plasma membrane	receptor activity				0																		---	---	---	---
RTN4RL1	146760	broad.mit.edu	37	17	1921003	1921004	+	Intron	INS	-	CACG	CACG	rs149316759	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1921003_1921004insCACG	uc002ftp.2	-						uc002ftq.2_5'Flank	NM_178568	NP_848663			reticulon 4 receptor-like 1 precursor						axon regeneration	anchored to plasma membrane	receptor activity				0																		---	---	---	---
SMG6	23293	broad.mit.edu	37	17	2188968	2188968	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2188968delT	uc002fub.1	-							NM_017575	NP_060045			Smg-6 homolog, nonsense mediated mRNA decay						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation|telomere maintenance	chromosome, telomeric region|cytosol|nucleolus|telomerase holoenzyme complex	endoribonuclease activity|metal ion binding|protein binding|telomeric DNA binding			central_nervous_system(2)|lung(1)|kidney(1)	4																		---	---	---	---
TSR1	55720	broad.mit.edu	37	17	2228903	2228903	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2228903delT	uc002fuj.2	-							NM_018128	NP_060598			TSR1, 20S rRNA accumulation						ribosome assembly	nucleolus	protein binding			ovary(1)	1																		---	---	---	---
SGSM2	9905	broad.mit.edu	37	17	2280315	2280315	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2280315delG	uc002fun.3	+	20	2795	c.2620delG	c.(2620-2622)GGGfs	p.G874fs	SGSM2_uc002fum.3_Frame_Shift_Del_p.G919fs|SGSM2_uc010vqw.1_Frame_Shift_Del_p.G874fs|SGSM2_uc002fup.1_Frame_Shift_Del_p.G52fs|SGSM2_uc002fuq.2_Frame_Shift_Del_p.G36fs	NM_001098509	NP_001091979	O43147	SGSM2_HUMAN	RUN and TBC1 domain containing 1 isoform 2	874	Rab-GAP TBC.					intracellular	Rab GTPase activator activity				0				Colorectal(2;5.15e-05)|READ - Rectum adenocarcinoma(2;0.000115)														---	---	---	---
PAFAH1B1	5048	broad.mit.edu	37	17	2506461	2506461	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2506461delT	uc002fuw.3	+						PAFAH1B1_uc010ckb.1_Intron	NM_000430	NP_000421			platelet-activating factor acetylhydrolase,						acrosome assembly|actin cytoskeleton organization|adult locomotory behavior|brain morphogenesis|corpus callosum morphogenesis|establishment of mitotic spindle orientation|G2/M transition of mitotic cell cycle|hippocampus development|layer formation in cerebral cortex|learning or memory|lipid catabolic process|microtubule organizing center organization|mitotic prometaphase|neuroblast proliferation|neuromuscular process controlling balance|neuron migration|platelet activating factor metabolic process|regulation of Rho GTPase activity|retrograde axon cargo transport|synaptic transmission|vesicle transport along microtubule	astral microtubule|cell cortex|centrosome|cytosol|kinetochore|motile primary cilium|nuclear membrane|perinuclear region of cytoplasm	dynactin binding|heparin binding|microtubule binding|phospholipase binding|phosphoprotein binding|protein homodimerization activity			skin(1)	1																		---	---	---	---
PAFAH1B1	5048	broad.mit.edu	37	17	2559742	2559743	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2559742_2559743delTT	uc002fuw.3	+						PAFAH1B1_uc010ckb.1_Intron	NM_000430	NP_000421			platelet-activating factor acetylhydrolase,						acrosome assembly|actin cytoskeleton organization|adult locomotory behavior|brain morphogenesis|corpus callosum morphogenesis|establishment of mitotic spindle orientation|G2/M transition of mitotic cell cycle|hippocampus development|layer formation in cerebral cortex|learning or memory|lipid catabolic process|microtubule organizing center organization|mitotic prometaphase|neuroblast proliferation|neuromuscular process controlling balance|neuron migration|platelet activating factor metabolic process|regulation of Rho GTPase activity|retrograde axon cargo transport|synaptic transmission|vesicle transport along microtubule	astral microtubule|cell cortex|centrosome|cytosol|kinetochore|motile primary cilium|nuclear membrane|perinuclear region of cytoplasm	dynactin binding|heparin binding|microtubule binding|phospholipase binding|phosphoprotein binding|protein homodimerization activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	2656111	2656111	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2656111delT								MIR1253 (4635 upstream) : RAP1GAP2 (43621 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	3156356	3156361	+	IGR	DEL	CTCTCA	-	-	rs71924759		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3156356_3156361delCTCTCA								OR1A1 (36514 upstream) : OR3A2 (24824 downstream)																																			---	---	---	---
ITGAE	3682	broad.mit.edu	37	17	3678243	3678243	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3678243delT	uc002fwo.3	-							NM_002208	NP_002199			integrin, alpha E precursor						cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			large_intestine(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)														---	---	---	---
CAMKK1	84254	broad.mit.edu	37	17	3773614	3773614	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3773614delC	uc002fwt.2	-						CAMKK1_uc002fwu.2_Intron|CAMKK1_uc002fwv.2_Intron	NM_172206	NP_757343			calcium/calmodulin-dependent protein kinase 1						synaptic transmission	cytosol|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)	1				LUAD - Lung adenocarcinoma(2;2.11e-05)|Lung(3;0.0176)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	3894125	3894127	+	IGR	DEL	CTC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3894125_3894127delCTC								ATP2A3 (26389 upstream) : ZZEF1 (13613 downstream)																																			---	---	---	---
ZZEF1	23140	broad.mit.edu	37	17	4035073	4035073	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4035073delA	uc002fxe.2	-						ZZEF1_uc002fxk.1_Intron	NM_015113	NP_055928			zinc finger, ZZ type with EF hand domain 1								calcium ion binding|zinc ion binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
ANKFY1	51479	broad.mit.edu	37	17	4120982	4120983	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4120982_4120983delTT	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																		---	---	---	---
UBE2G1	7326	broad.mit.edu	37	17	4220652	4220652	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4220652delA	uc002fxs.2	-							NM_003342	NP_003333			ubiquitin-conjugating enzyme E2G 1						protein K48-linked ubiquitination|protein K63-linked ubiquitination|ubiquitin-dependent protein catabolic process		ATP binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity				0																		---	---	---	---
UBE2G1	7326	broad.mit.edu	37	17	4266569	4266569	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4266569delA	uc002fxs.2	-							NM_003342	NP_003333			ubiquitin-conjugating enzyme E2G 1						protein K48-linked ubiquitination|protein K63-linked ubiquitination|ubiquitin-dependent protein catabolic process		ATP binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity				0																		---	---	---	---
SPNS3	201305	broad.mit.edu	37	17	4342236	4342237	+	Intron	DEL	TG	-	-	rs143375676		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4342236_4342237delTG	uc002fxt.2	+						SPNS3_uc002fxu.2_Intron	NM_182538	NP_872344			spinster homolog 3						lipid transport|transmembrane transport	integral to membrane				large_intestine(1)	1																		---	---	---	---
PLD2	5338	broad.mit.edu	37	17	4714407	4714426	+	Intron	DEL	CATTGATCTCTCTGATTTCG	-	-	rs113274766		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4714407_4714426delCATTGATCTCTCTGATTTCG	uc002fzc.2	+						PLD2_uc010vsj.1_Intron|PLD2_uc002fzd.2_Intron	NM_002663	NP_002654			phospholipase D2						cell communication|cytoskeleton organization|small GTPase mediated signal transduction		NAPE-specific phospholipase D activity|phosphatidylinositol binding|phospholipase D activity			breast(2)|upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	5					Choline(DB00122)													---	---	---	---
CAMTA2	23125	broad.mit.edu	37	17	4875738	4875738	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4875738delG	uc002gah.1	-	16	2705	c.2597delC	c.(2596-2598)CCTfs	p.P866fs	CAMTA2_uc010cku.1_Frame_Shift_Del_p.P889fs|CAMTA2_uc002gag.1_Frame_Shift_Del_p.P865fs|CAMTA2_uc002gai.1_Frame_Shift_Del_p.P868fs|CAMTA2_uc010ckv.1_Frame_Shift_Del_p.P513fs	NM_015099	NP_055914	O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2	866					cardiac muscle hypertrophy in response to stress|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	calmodulin binding|chromatin binding|histone deacetylase binding|transcription factor binding			ovary(1)	1																		---	---	---	---
USP6	9098	broad.mit.edu	37	17	5044641	5044642	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5044641_5044642delAA	uc002gau.1	+						USP6_uc002gav.1_Intron|USP6_uc010ckz.1_Intron	NM_004505	NP_004496			ubiquitin specific protease 6						protein deubiquitination|regulation of vesicle-mediated transport|ubiquitin-dependent protein catabolic process	lysosome|plasma membrane|recycling endosome	calmodulin binding|cysteine-type endopeptidase activity|nucleic acid binding|protein binding|Rab GTPase activator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			skin(2)|upper_aerodigestive_tract(1)|lung(1)|breast(1)	5								T	COL1A1|CDH11|ZNF9|OMD	aneurysmal bone cysts								---	---	---	---
USP6	9098	broad.mit.edu	37	17	5047792	5047792	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5047792delT	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								---	---	---	---
Unknown	0	broad.mit.edu	37	17	5096766	5096766	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5096766delA	uc002gbf.1	+						uc002gbg.1_Intron|ZNF594_uc010cla.1_5'Flank					Homo sapiens cDNA FLJ11816 fis, clone HEMBA1006416.																														---	---	---	---
C17orf87	388325	broad.mit.edu	37	17	5134656	5134656	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5134656delA	uc002gbh.2	-						uc002gbg.1_Intron|C17orf87_uc010clb.1_Intron|C17orf87_uc002gbi.2_Intron	NM_207103	NP_996986			hypothetical protein LOC388325							integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	5145070	5145070	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5145070delA								C17orf87 (6987 upstream) : RABEP1 (40488 downstream)																																			---	---	---	---
DHX33	56919	broad.mit.edu	37	17	5368578	5368578	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5368578delT	uc002gca.2	-						DHX33_uc002gcb.2_Intron|DHX33_uc010clf.2_Intron	NM_020162	NP_064547			DEAH (Asp-Glu-Ala-His) box polypeptide 33							nucleolus	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	5703368	5703368	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5703368delT	uc002gcm.2	+											Homo sapiens hypothetical protein LOC339166, mRNA (cDNA clone IMAGE:5163423), partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	6579512	6579513	+	IGR	DEL	CA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6579512_6579513delCA								C17orf100 (22895 upstream) : SLC13A5 (8528 downstream)																																	OREG0031454	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	---	---	---	---
ASGR2	433	broad.mit.edu	37	17	7016870	7016871	+	Intron	INS	-	CACT	CACT			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7016870_7016871insCACT	uc002gep.3	-						ASGR2_uc002gem.1_Intron|ASGR2_uc002gen.1_Intron|ASGR2_uc002geo.1_Intron|ASGR2_uc002ger.3_Intron|ASGR2_uc002geq.3_Intron|ASGR2_uc010clw.2_Intron|ASGR2_uc010vtl.1_Intron	NM_001181	NP_001172			asialoglycoprotein receptor 2 isoform a						cell surface receptor linked signaling pathway|endocytosis	focal adhesion|integral to membrane|nucleolus	asialoglycoprotein receptor activity|protein binding|sugar binding			ovary(1)	1					Antihemophilic Factor(DB00025)													---	---	---	---
Unknown	0	broad.mit.edu	37	17	7208413	7208413	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7208413delT								YBX2 (10537 upstream) : EIF5A (1905 downstream)																																			---	---	---	---
WRAP53	55135	broad.mit.edu	37	17	7603866	7603866	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7603866delA	uc010vuh.1	+						WRAP53_uc010vui.1_Intron|WRAP53_uc002gip.2_Intron|WRAP53_uc002gir.2_Intron|WRAP53_uc002giq.2_Intron|WRAP53_uc010cnl.2_Intron|WRAP53_uc010vuj.1_5'Flank	NM_001143990	NP_001137462			WD repeat domain 79 isoform 2						positive regulation of telomerase activity|telomere formation via telomerase	Cajal body|cytoplasm|telomerase holoenzyme complex	protein binding|RNA binding				0																		---	---	---	---
NDEL1	81565	broad.mit.edu	37	17	8352084	8352084	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8352084delT	uc002glj.2	+						NDEL1_uc002gli.2_Intron	NM_030808	NP_110435			nudE nuclear distribution gene E homolog (A.						chromosome segregation|mitotic prometaphase	condensed chromosome kinetochore|cytosol|microtubule|spindle					0																		---	---	---	---
NDEL1	81565	broad.mit.edu	37	17	8353447	8353447	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8353447delA	uc002glj.2	+						NDEL1_uc002gli.2_Intron	NM_030808	NP_110435			nudE nuclear distribution gene E homolog (A.						chromosome segregation|mitotic prometaphase	condensed chromosome kinetochore|cytosol|microtubule|spindle					0																		---	---	---	---
MYH10	4628	broad.mit.edu	37	17	8390665	8390665	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8390665delC	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																		---	---	---	---
MYH10	4628	broad.mit.edu	37	17	8508327	8508327	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8508327delA	uc002gll.2	-						MYH10_uc002glm.2_Intron|MYH10_uc010cnx.2_Intron	NM_005964	NP_005955			myosin, heavy polypeptide 10, non-muscle						actin filament-based movement|axon guidance|cytokinesis after mitosis|regulation of cell shape	cell cortex|cleavage furrow|midbody|myosin complex|stress fiber	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(2)	2																		---	---	---	---
PIK3R5	23533	broad.mit.edu	37	17	8812614	8812615	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8812614_8812615delTT	uc002glt.2	-						PIK3R5_uc010vuz.1_Intron|PIK3R5_uc002glu.3_Intron|PIK3R5_uc010coa.1_Intron|PIK3R5_uc010cob.1_Intron	NM_014308	NP_055123			phosphoinositide-3-kinase, regulatory subunit 5						platelet activation	cytosol|membrane|nucleus				breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
NTN1	9423	broad.mit.edu	37	17	8941525	8941526	+	Intron	INS	-	CT	CT	rs140463294	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8941525_8941526insCT	uc002glw.3	+							NM_004822	NP_004813			netrin 1 precursor						apoptosis|axon guidance		protein binding				0																		---	---	---	---
STX8	9482	broad.mit.edu	37	17	9196788	9196790	+	Intron	DEL	TTT	-	-	rs111288273		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9196788_9196790delTTT	uc002glx.2	-							NM_004853	NP_004844			syntaxin 8						transport	endoplasmic reticulum|integral to plasma membrane				central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	9642218	9642218	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9642218delT								USP43 (9217 upstream) : DHRS7C (32538 downstream)																																			---	---	---	---
GAS7	8522	broad.mit.edu	37	17	10090206	10090206	+	Intron	DEL	A	-	-	rs35082694		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10090206delA	uc002gmg.1	-							NM_201433	NP_958839			growth arrest-specific 7 isoform c						cell cycle arrest	cytoplasm	sequence-specific DNA binding transcription factor activity			lung(1)|pancreas(1)	2								T	MLL	AML*								---	---	---	---
MYH13	8735	broad.mit.edu	37	17	10216089	10216089	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10216089delT	uc002gmk.1	-							NM_003802	NP_003793			myosin, heavy polypeptide 13, skeletal muscle						muscle contraction	muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|skin(2)	6																		---	---	---	---
MYH8	4626	broad.mit.edu	37	17	10305949	10305950	+	Intron	DEL	CA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10305949_10305950delCA	uc002gmm.2	-						uc002gml.1_Intron	NM_002472	NP_002463			myosin, heavy chain 8, skeletal muscle,						muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			skin(6)|ovary(3)|breast(2)	11														Trismus-Pseudocamptodactyly_Syndrome_with_Cardiac_Myxoma_and_Freckling				---	---	---	---
MYH2	4620	broad.mit.edu	37	17	10446506	10446506	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10446506delT	uc010coi.2	-						uc002gml.1_Intron|MYH2_uc002gmp.3_Intron|MYH2_uc010coj.2_Intron	NM_001100112	NP_001093582			myosin heavy chain IIa						muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1)	14																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	10531668	10531668	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10531668delT								MYH2 (78651 upstream) : MYH3 (175 downstream)																																			---	---	---	---
SHISA6	388336	broad.mit.edu	37	17	11300712	11300713	+	Intron	INS	-	TGTG	TGTG	rs71869492		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11300712_11300713insTGTG	uc002gna.3	+						SHISA6_uc002gnb.3_Intron|SHISA6_uc010com.2_Intron	NM_207386	NP_997269			shisa homolog 6							integral to membrane				breast(1)	1																		---	---	---	---
SHISA6	388336	broad.mit.edu	37	17	11300992	11300992	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11300992delT	uc002gna.3	+						SHISA6_uc002gnb.3_Intron|SHISA6_uc010com.2_Intron	NM_207386	NP_997269			shisa homolog 6							integral to membrane				breast(1)	1																		---	---	---	---
MAP2K4	6416	broad.mit.edu	37	17	11936453	11936453	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11936453delA	uc002gnj.2	+						MAP2K4_uc002gnk.2_Intron	NM_003010	NP_003001			mitogen-activated protein kinase kinase 4						cellular response to mechanical stimulus|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|JUN kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			large_intestine(14)|breast(12)|lung(8)|ovary(8)|pancreas(8)|stomach(2)|central_nervous_system(1)|biliary_tract(1)|testis(1)|endometrium(1)|urinary_tract(1)|skin(1)	58		all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163)		Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681)				D|Mis|N		pancreatic|breast|colorectal								---	---	---	---
Unknown	0	broad.mit.edu	37	17	12493507	12493507	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12493507delA	uc002gnl.1	+						uc002gnm.1_Intron					Homo sapiens cDNA FLJ34690 fis, clone MESAN2000894.																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	13090645	13090645	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13090645delT								ELAC2 (169286 upstream) : HS3ST3A1 (308361 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	14160883	14160884	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14160883_14160884delTT								CDRT15 (20704 upstream) : HS3ST3B1 (43622 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	14197371	14197371	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14197371delA								CDRT15 (57192 upstream) : HS3ST3B1 (7135 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	14546260	14546260	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14546260delA								HS3ST3B1 (296768 upstream) : PMP22 (586837 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	14720161	14720161	+	IGR	DEL	G	-	-	rs112062858		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14720161delG								HS3ST3B1 (470669 upstream) : PMP22 (412936 downstream)																																			---	---	---	---
PMP22	5376	broad.mit.edu	37	17	15148415	15148415	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15148415delA	uc002goj.2	-						PMP22_uc002gok.2_Intron|PMP22_uc002gol.2_Intron	NM_153322	NP_696997			peripheral myelin protein 22						peripheral nervous system development|synaptic transmission	integral to membrane					0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0884)|BRCA - Breast invasive adenocarcinoma(8;4.92e-06)														---	---	---	---
TRIM16	10626	broad.mit.edu	37	17	15508389	15508389	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15508389delA	uc002gor.1	-						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)														---	---	---	---
TRIM16	10626	broad.mit.edu	37	17	15517512	15517512	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15517512delT	uc002gor.1	-						CDRT1_uc002gov.3_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)														---	---	---	---
CENPV	201161	broad.mit.edu	37	17	16253229	16253229	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16253229delA	uc002gpw.2	-							NM_181716	NP_859067			proline rich 6						cell division|centromeric heterochromatin formation|mitosis|positive regulation of cytokinesis|regulation of chromosome organization	condensed chromosome kinetochore|cytoplasm|nucleus|spindle midzone	carbon-sulfur lyase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	16720131	16720131	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16720131delA								LOC162632 (12312 upstream) : TNFRSF13B (112718 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	17337149	17337149	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17337149delA								NT5M (86174 upstream) : MED9 (43151 downstream)																																			---	---	---	---
TOM1L2	146691	broad.mit.edu	37	17	17753827	17753828	+	Intron	DEL	AC	-	-	rs12941550	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17753827_17753828delAC	uc002grz.3	-						TOM1L2_uc002gry.3_Intron|TOM1L2_uc010vwy.1_Intron|TOM1L2_uc010cpr.2_Intron|TOM1L2_uc010vwz.1_Intron|TOM1L2_uc010vxa.1_Intron|TOM1L2_uc002grv.3_Intron	NM_001082968	NP_001076437			target of myb1-like 2 isoform 3						intracellular protein transport	intracellular					0	all_neural(463;0.228)																	---	---	---	---
LRRC48	83450	broad.mit.edu	37	17	17903614	17903615	+	Intron	DEL	GT	-	-	rs68125224		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17903614_17903615delGT	uc010vxd.1	+						LRRC48_uc002gsa.2_Intron|LRRC48_uc010vxc.1_Intron|LRRC48_uc002gsb.2_Intron|LRRC48_uc010vxe.1_Intron	NM_001130090	NP_001123562			leucine rich repeat containing 48 isoform a							cytoplasm				pancreas(1)	1	all_neural(463;0.228)																	---	---	---	---
Unknown	0	broad.mit.edu	37	17	18307794	18307794	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18307794delA								EVPLL (14836 upstream) : LOC339240 (15488 downstream)																																			---	---	---	---
PRPSAP2	5636	broad.mit.edu	37	17	18757040	18757041	+	5'Flank	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18757040_18757041delAA	uc010vyi.1	+						PRPSAP2_uc002guo.1_5'Flank	NM_002767	NP_002758			phosphoribosyl pyrophosphate						nucleotide biosynthetic process		enzyme inhibitor activity|magnesium ion binding|ribose phosphate diphosphokinase activity			skin(1)	1																		---	---	---	---
PRPSAP2	5636	broad.mit.edu	37	17	18832049	18832049	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18832049delT	uc002gup.1	+						PRPSAP2_uc002guo.1_Intron|PRPSAP2_uc010vyi.1_Intron|PRPSAP2_uc010vyj.1_Intron|PRPSAP2_uc010vyk.1_Intron|PRPSAP2_uc002guq.1_Frame_Shift_Del_p.F31fs	NM_002767	NP_002758			phosphoribosyl pyrophosphate						nucleotide biosynthetic process		enzyme inhibitor activity|magnesium ion binding|ribose phosphate diphosphokinase activity			skin(1)	1																		---	---	---	---
RNF112	7732	broad.mit.edu	37	17	19316728	19316729	+	Intron	INS	-	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19316728_19316729insG	uc010vyw.1	+						RNF112_uc010vyv.1_Intron|RNF112_uc010vyx.1_Intron	NM_007148	NP_009079			ring finger protein 112								GTP binding|GTPase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
AKAP10	11216	broad.mit.edu	37	17	19847967	19847970	+	Intron	DEL	AAAC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19847967_19847970delAAAC	uc002gwo.2	-						AKAP10_uc002gwp.1_Intron|AKAP10_uc010cqw.1_Intron	NM_007202	NP_009133			A-kinase anchor protein 10 precursor						blood coagulation|protein localization	cytosol|mitochondrion|plasma membrane	signal transducer activity			skin(1)	1	all_cancers(12;2.08e-05)|all_epithelial(12;0.00158)|Breast(13;0.165)																	---	---	---	---
CCDC144C	348254	broad.mit.edu	37	17	20233890	20233892	+	Intron	DEL	TTG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20233890_20233892delTTG	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	20634737	20634737	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20634737delT								LGALS9B (263889 upstream) : CCDC144NL (131973 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	20671295	20671295	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20671295delA								LGALS9B (300447 upstream) : CCDC144NL (95415 downstream)																																			---	---	---	---
MAP2K3	5606	broad.mit.edu	37	17	21217018	21217020	+	Intron	DEL	CCT	-	-	rs72412380		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21217018_21217020delCCT	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	21406523	21406524	+	IGR	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21406523_21406524delGT								KCNJ12 (83344 upstream) : C17orf51 (25048 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21487135	21487135	+	IGR	DEL	A	-	-	rs112673625		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21487135delA								C17orf51 (9404 upstream) : FAM27L (338235 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21853029	21853029	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21853029delA								FAM27L (26526 upstream) : FLJ36000 (51033 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	22218924	22218924	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:22218924delT								FLJ36000 (305854 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25318507	25318507	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25318507delC								None (None upstream) : WSB1 (302599 downstream)																																			---	---	---	---
KSR1	8844	broad.mit.edu	37	17	25840454	25840454	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25840454delA	uc010crg.2	+						KSR1_uc002gzj.1_Intron	NM_014238	NP_055053			kinase suppressor of ras						Ras protein signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|central_nervous_system(1)	4	Lung NSC(42;0.00836)		BRCA - Breast invasive adenocarcinoma(3;0.00122)	UCEC - Uterine corpus endometrioid carcinoma (53;0.168)														---	---	---	---
NOS2	4843	broad.mit.edu	37	17	26190255	26190255	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26190255delA	uc010crh.1	-							NM_000625	NP_000616			nitric oxide synthase 2A						arginine catabolic process|defense response to Gram-negative bacterium|innate immune response in mucosa|nitric oxide biosynthetic process|peptidyl-cysteine S-nitrosylation|platelet activation|positive regulation of killing of cells of other organism|positive regulation of leukocyte mediated cytotoxicity|regulation of cellular respiration|regulation of insulin secretion|superoxide metabolic process	cytosol|nucleus	arginine binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|protein homodimerization activity|tetrahydrobiopterin binding			skin(2)|ovary(1)|breast(1)	4					Dexamethasone(DB01234)|Hydrocortisone(DB00741)|L-Arginine(DB00125)|L-Citrulline(DB00155)													---	---	---	---
Unknown	0	broad.mit.edu	37	17	26349094	26349094	+	IGR	DEL	A	-	-	rs113183505		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26349094delA								NOS2 (128685 upstream) : NLK (20594 downstream)																																			---	---	---	---
NLK	51701	broad.mit.edu	37	17	26512302	26512302	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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)														---	---	---	---
SLC46A1	113235	broad.mit.edu	37	17	26732680	26732681	+	Intron	INS	-	C	C	rs41297079		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26732680_26732681insC	uc002hbf.1	-						SLC46A1_uc002hbg.1_Intron|SLC46A1_uc010wak.1_Intron	NM_080669	NP_542400			proton-coupled folate transporter						cellular iron ion homeostasis|folic acid metabolic process	apical plasma membrane|cytoplasm|integral to membrane	folic acid binding|folic acid transporter activity|heme transporter activity				0	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Folic Acid(DB00158)													---	---	---	---
Unknown	0	broad.mit.edu	37	17	26791144	26791144	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26791144delA								SLC46A1 (57916 upstream) : SLC13A2 (9520 downstream)																																			---	---	---	---
SPAG5	10615	broad.mit.edu	37	17	26923218	26923219	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26923218_26923219insA	uc002hbq.2	-						SGK494_uc010waq.1_Intron	NM_006461	NP_006452			sperm associated antigen 5						cell division|mitosis|phosphatidylinositol-mediated signaling|spindle organization	condensed chromosome kinetochore|cytoplasm|spindle pole	protein binding			central_nervous_system(1)	1	Lung NSC(42;0.00431)																	---	---	---	---
KIAA0100	9703	broad.mit.edu	37	17	26969669	26969669	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26969669delA	uc002hbu.2	-						KIAA0100_uc002hbv.2_Intron|KIAA0100_uc010crr.1_Intron	NM_014680	NP_055495			hypothetical protein LOC9703 precursor							extracellular region				ovary(2)|breast(1)|skin(1)	4	Lung NSC(42;0.00431)																	---	---	---	---
SUPT6H	6830	broad.mit.edu	37	17	27004564	27004565	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27004564_27004565delAA	uc002hby.2	+						SUPT6H_uc010crt.2_Intron	NM_003170	NP_003161			suppressor of Ty 6 homolog						chromatin remodeling|regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter	nucleus	hydrolase activity, acting on ester bonds|RNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3	Lung NSC(42;0.00431)																	---	---	---	---
C17orf63	55731	broad.mit.edu	37	17	27115259	27115259	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27115259delT	uc002hct.1	-						C17orf63_uc010wax.1_Intron|C17orf63_uc010way.1_Intron|C17orf63_uc002hcw.2_Intron	NM_018182	NP_060652			hypothetical protein LOC55731											ovary(1)	1	all_epithelial(6;5.06e-20)|Lung NSC(42;0.01)		Epithelial(11;3.38e-06)|all cancers(11;2.46e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.104)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	27644984	27644984	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27644984delA								NUFIP2 (23818 upstream) : TAOK1 (72959 downstream)																																			---	---	---	---
TAOK1	57551	broad.mit.edu	37	17	27848044	27848044	+	Intron	DEL	A	-	-	rs76943515		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27848044delA	uc002hdz.1	+						TAOK1_uc010wbe.1_Intron|TAOK1_uc010wbf.1_Intron	NM_020791	NP_065842			TAO kinase 1						mitotic prometaphase	cytosol|intracellular membrane-bounded organelle	ATP binding|protein serine/threonine kinase activity			upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)|skin(1)	4			Colorectal(6;0.198)															---	---	---	---
SSH2	85464	broad.mit.edu	37	17	27979167	27979167	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27979167delA	uc002heo.1	-						SSH2_uc010wbh.1_Intron|SSH2_uc002hep.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	28109611	28109611	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28109611delT	uc002heo.1	-						SSH2_uc010wbh.1_Intron|SSH2_uc002hep.1_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																		---	---	---	---
CCDC55	84081	broad.mit.edu	37	17	28503103	28503104	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28503103_28503104insT	uc002heu.2	+						CCDC55_uc002hev.2_Intron|CCDC55_uc010wbl.1_Intron|CCDC55_uc010wbm.1_Intron|CCDC55_uc002hex.2_Intron	NM_032141	NP_115517			coiled-coil domain containing 55 isoform 1						developmental process|nucleocytoplasmic transport|regulation of alternative nuclear mRNA splicing, via spliceosome	nuclear speck|ribonucleoprotein complex	mRNA binding|protein binding				0																		---	---	---	---
LRRC37B2	147172	broad.mit.edu	37	17	28911210	28911210	+	Intron	DEL	A	-	-	rs74377021		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28911210delA	uc010wbq.1	+							NR_015341				Homo sapiens cDNA FLJ90801 fis, clone Y79AA1000207.												0																		---	---	---	---
ATAD5	79915	broad.mit.edu	37	17	29163151	29163151	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29163151delT	uc002hfs.1	+						ATAD5_uc002hft.1_Intron	NM_024857	NP_079133			ATPase family, AAA domain containing 5						response to DNA damage stimulus	nucleus	ATP binding|nucleoside-triphosphatase activity			ovary(3)	3		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)																---	---	---	---
ATAD5	79915	broad.mit.edu	37	17	29185289	29185289	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29185289delA	uc002hfs.1	+	9	3250	c.2904delA	c.(2902-2904)CTAfs	p.L968fs	ATAD5_uc002hft.1_Frame_Shift_Del_p.L865fs	NM_024857	NP_079133	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	968					response to DNA damage stimulus	nucleus	ATP binding|nucleoside-triphosphatase activity			ovary(3)	3		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)																---	---	---	---
ATAD5	79915	broad.mit.edu	37	17	29222011	29222011	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29222011delA	uc002hfs.1	+	23						NM_024857	NP_079133			ATPase family, AAA domain containing 5						response to DNA damage stimulus	nucleus	ATP binding|nucleoside-triphosphatase activity			ovary(3)	3		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	30148213	30148213	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30148213delT								MIR365-2 (245673 upstream) : C17orf79 (30672 downstream)																																			---	---	---	---
SUZ12	23512	broad.mit.edu	37	17	30267580	30267580	+	Intron	DEL	A	-	-	rs67854327		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30267580delA	uc002hgs.2	+						SUZ12_uc002hgt.2_Intron	NM_015355	NP_056170			joined to JAZF1						negative regulation of cell differentiation|transcription, DNA-dependent	ESC/E(Z) complex	histone methyltransferase activity|methylated histone residue binding|zinc ion binding		JAZF1/SUZ12(131)	soft_tissue(98)|endometrium(33)	131		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.041)|Ovarian(249;0.182)|Breast(31;0.231)						T	JAZF1	endometrial stromal tumours								---	---	---	---
Unknown	0	broad.mit.edu	37	17	30456803	30456804	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30456803_30456804delTT								LRRC37B (76286 upstream) : RHOT1 (12669 downstream)																																			---	---	---	---
MYO1D	4642	broad.mit.edu	37	17	31103177	31103177	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31103177delA	uc002hho.1	-						MYO1D_uc002hhp.1_Intron|MYO1D_uc010wcb.1_Intron	NM_015194	NP_056009			myosin ID							myosin complex	actin binding|ATP binding|calmodulin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3			BRCA - Breast invasive adenocarcinoma(9;0.0362)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	31282844	31282844	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31282844delA								TMEM98 (14179 upstream) : SPACA3 (36038 downstream)																																			---	---	---	---
ACCN1	40	broad.mit.edu	37	17	31745039	31745060	+	Intron	DEL	TGTATGTATGTGTGTGTGTGTG	-	-	rs11275217		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31745039_31745060delTGTATGTATGTGTGTGTGTGTG	uc002hhu.2	-							NM_001094	NP_001085			amiloride-sensitive cation channel 1, neuronal						central nervous system development|peripheral nervous system development|synaptic transmission	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Breast(31;0.042)|Ovarian(249;0.202)		UCEC - Uterine corpus endometrioid carcinoma (308;0.13)|BRCA - Breast invasive adenocarcinoma(366;0.215)	Amiloride(DB00594)													---	---	---	---
ACCN1	40	broad.mit.edu	37	17	32371140	32371145	+	Intron	DEL	CACACG	-	-	rs58795616		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32371140_32371145delCACACG	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	32752651	32752653	+	IGR	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32752651_32752653delTTT								CCL1 (62399 upstream) : C17orf102 (148489 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	33162422	33162423	+	IGR	INS	-	CT	CT			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33162422_33162423insCT								TMEM132E (196086 upstream) : CCT6B (92517 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	33190951	33190951	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33190951delG								TMEM132E (224615 upstream) : CCT6B (63989 downstream)																																			---	---	---	---
FNDC8	54752	broad.mit.edu	37	17	33457239	33457240	+	Intron	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33457239_33457240delAG	uc002hix.2	+							NM_017559	NP_060029			fibronectin type III domain containing 8											ovary(2)	2		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.022)														---	---	---	---
MYO19	80179	broad.mit.edu	37	17	34856368	34856368	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34856368delA	uc010wcy.1	-						MYO19_uc002hmw.2_Intron|MYO19_uc010cuu.2_Intron	NM_001163735	NP_001157207			myosin XIX isoform 2							mitochondrial outer membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)	1		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)														---	---	---	---
PIGW	284098	broad.mit.edu	37	17	34894610	34894610	+	3'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34894610delT	uc002hmy.1	+	2					PIGW_uc002hmz.1_3'UTR	NM_178517	NP_848612			phosphatidylinositol glycan, class W						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	O-acyltransferase activity				0		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	35098577	35098578	+	IGR	DEL	GA	-	-	rs67820933		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35098577_35098578delGA								MRM1 (133171 upstream) : LHX1 (195921 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	35275387	35275387	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35275387delT								MRM1 (309981 upstream) : LHX1 (19112 downstream)																																			---	---	---	---
AATF	26574	broad.mit.edu	37	17	35346372	35346372	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35346372delT	uc002hni.2	+						AATF_uc002hnj.2_Intron	NM_012138	NP_036270			apoptosis antagonizing transcription factor						anti-apoptosis|apoptosis|induction of apoptosis by extracellular signals|negative regulation of superoxide anion generation|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to DNA damage stimulus	centrosome|focal adhesion|nucleolus	leucine zipper domain binding|sequence-specific DNA binding transcription factor activity				0		Breast(25;0.00607)																---	---	---	---
ACACA	31	broad.mit.edu	37	17	35593394	35593395	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35593394_35593395delTT	uc002hnm.2	-						ACACA_uc002hnk.2_Intron|ACACA_uc002hnl.2_Intron|ACACA_uc002hnn.2_Intron|ACACA_uc002hno.2_Intron|ACACA_uc010cuz.2_Intron	NM_198836	NP_942133			acetyl-Coenzyme A carboxylase alpha isoform 2						acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process	cytosol	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			large_intestine(1)|ovary(1)	2		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)													---	---	---	---
ACACA	31	broad.mit.edu	37	17	35646958	35646959	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35646958_35646959insT	uc002hnm.2	-						ACACA_uc002hnk.2_Intron|ACACA_uc002hnl.2_Intron|ACACA_uc002hnn.2_Intron|ACACA_uc002hno.2_Intron|ACACA_uc010cuz.2_Intron|ACACA_uc002hnq.2_Intron|ACACA_uc002hnp.1_Intron	NM_198836	NP_942133			acetyl-Coenzyme A carboxylase alpha isoform 2						acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process	cytosol	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			large_intestine(1)|ovary(1)	2		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)													---	---	---	---
TADA2A	6871	broad.mit.edu	37	17	35772870	35772870	+	Intron	DEL	A	-	-	rs75778569		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35772870delA	uc002hnt.2	+						TADA2A_uc002hnu.1_Intron|TADA2A_uc002hnv.2_Intron|TADA2A_uc010wdd.1_Intron	NM_001488	NP_001479			transcriptional adaptor 2A isoform a						histone H3 acetylation|transcription from RNA polymerase II promoter	chromosome|PCAF complex	DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity|zinc ion binding			breast(3)|skin(1)	4																		---	---	---	---
TADA2A	6871	broad.mit.edu	37	17	35832176	35832177	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35832176_35832177delTT	uc002hnt.2	+						TADA2A_uc002hnv.2_Intron|TADA2A_uc002hnw.2_Intron|TADA2A_uc010cvb.2_Intron	NM_001488	NP_001479			transcriptional adaptor 2A isoform a						histone H3 acetylation|transcription from RNA polymerase II promoter	chromosome|PCAF complex	DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity|zinc ion binding			breast(3)|skin(1)	4																		---	---	---	---
DUSP14	11072	broad.mit.edu	37	17	35872185	35872185	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35872185delA	uc002hnx.2	+						DUSP14_uc002hny.2_Intron|DUSP14_uc002hnz.2_Intron	NM_007026	NP_008957			dual specificity phosphatase 14								MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity				0		Breast(25;0.00637)|Ovarian(249;0.15)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	36010366	36010366	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36010366delA								DDX52 (6879 upstream) : HNF1B (36069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	36132465	36132466	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36132465_36132466delAA								HNF1B (27369 upstream) : LOC284100 (70107 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	36304010	36304010	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36304010delA								TBC1D3 (8912 upstream) : MRPL45 (148988 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	36331304	36331305	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36331304_36331305delTT								TBC1D3 (36206 upstream) : MRPL45 (121693 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	36831924	36831924	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36831924delC								C17orf96 (737 upstream) : MLLT6 (29949 downstream)																																			---	---	---	---
CWC25	54883	broad.mit.edu	37	17	36983467	36983468	+	5'Flank	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36983467_36983468insA	uc002hqu.2	-						CWC25_uc010wdv.1_5'Flank|CWC25_uc010wdx.1_5'Flank	NM_017748	NP_060218			coiled-coil domain containing 49												0																		---	---	---	---
RPL19	6143	broad.mit.edu	37	17	37358419	37358420	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37358419_37358420insT	uc002hrq.1	+						RPL19_uc002hrr.1_Intron	NM_000981	NP_000972			ribosomal protein L19						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	RNA binding|structural constituent of ribosome				0																		---	---	---	---
FBXL20	84961	broad.mit.edu	37	17	37423530	37423530	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37423530delA	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)															---	---	---	---
FBXL20	84961	broad.mit.edu	37	17	37534288	37534288	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37534288delA	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)															---	---	---	---
PGAP3	93210	broad.mit.edu	37	17	37838174	37838174	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37838174delA	uc002hsj.2	-						PGAP3_uc010cvy.2_Intron|PGAP3_uc010wej.1_Intron|PGAP3_uc002hsk.2_Intron|PGAP3_uc010cvz.2_Intron	NM_033419	NP_219487			per1-like domain containing 1 precursor						GPI anchor biosynthetic process	Golgi membrane|integral to membrane|intrinsic to endoplasmic reticulum membrane	hydrolase activity, acting on ester bonds			upper_aerodigestive_tract(1)	1																		---	---	---	---
GRB7	2886	broad.mit.edu	37	17	37902870	37902872	+	Intron	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37902870_37902872delAAA	uc002hsr.2	+						GRB7_uc002hss.2_Intron|GRB7_uc010cwc.2_Intron|GRB7_uc002hst.2_Intron	NM_005310	NP_005301			growth factor receptor-bound protein 7						blood coagulation|epidermal growth factor receptor signaling pathway|leukocyte migration|negative regulation of translation|positive regulation of cell migration|stress granule assembly	cytosol|focal adhesion|stress granule	phosphatidylinositol binding|protein kinase binding|SH3/SH2 adaptor activity			lung(2)|ovary(1)|breast(1)|skin(1)	5	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;6.86e-60)|all cancers(3;1.65e-53)|BRCA - Breast invasive adenocarcinoma(8;2.03e-43)|STAD - Stomach adenocarcinoma(3;1.43e-12)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	37919155	37919155	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37919155delA								GRB7 (15618 upstream) : IKZF3 (2046 downstream)																																			---	---	---	---
CASC3	22794	broad.mit.edu	37	17	38309573	38309573	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38309573delT	uc010cwt.1	+						CASC3_uc010cws.1_Intron|CASC3_uc002hue.2_Intron	NM_007359	NP_031385			metastatic lymph node 51						mRNA processing|mRNA transport|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translation|response to stress|RNA splicing	exon-exon junction complex|nuclear speck|perinuclear region of cytoplasm	identical protein binding|RNA binding|ubiquitin protein ligase binding			ovary(1)	1																		---	---	---	---
TOP2A	7153	broad.mit.edu	37	17	38576064	38576064	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38576064delT	uc002huq.2	-							NM_001067	NP_001058			DNA topoisomerase II, alpha isozyme						apoptotic chromosome condensation|DNA ligation|DNA repair|DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|phosphatidylinositol-mediated signaling|positive regulation of apoptosis|positive regulation of retroviral genome replication|resolution of meiotic recombination intermediates|sister chromatid segregation	cytoplasm|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex	ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|drug binding|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein homodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity|ubiquitin binding			ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Gatifloxacin(DB01044)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)													---	---	---	---
Unknown	0	broad.mit.edu	37	17	39301691	39301692	+	IGR	INS	-	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39301691_39301692insG								KRTAP4-12 (21272 upstream) : KRTAP4-5 (3486 downstream)																																			---	---	---	---
KRT37	8688	broad.mit.edu	37	17	39583421	39583421	+	5'Flank	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39583421delA	uc002hwp.1	-							NM_003770	NP_003761			keratin 37							intermediate filament	structural molecule activity			skin(1)	1		Breast(137;0.000496)																---	---	---	---
DHX58	79132	broad.mit.edu	37	17	40258179	40258179	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40258179delA	uc002hyw.3	-						DHX58_uc002hyv.3_Intron|DHX58_uc010wgf.1_Intron	NM_024119	NP_077024			RNA helicase LGP2						innate immune response	cytoplasm	ATP binding|DNA binding|helicase activity|protein binding|RNA binding|zinc ion binding				0		all_cancers(22;9.73e-07)|all_epithelial(22;3.58e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)														---	---	---	---
STAT3	6774	broad.mit.edu	37	17	40491111	40491112	+	Intron	DEL	TT	-	-	rs113555167		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40491111_40491112delTT	uc002hzl.1	-						STAT3_uc002hzk.1_Intron|STAT3_uc002hzm.1_Intron|STAT3_uc010wgh.1_Intron|STAT3_uc002hzn.1_Intron	NM_139276	NP_644805			signal transducer and activator of transcription						cellular component movement|eating behavior|eye photoreceptor cell differentiation|glucose homeostasis|interleukin-6-mediated signaling pathway|interspecies interaction between organisms|JAK-STAT cascade involved in growth hormone signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|protein import into nucleus|response to estradiol stimulus|sexual reproduction|temperature homeostasis	cytosol|nucleus|plasma membrane	calcium ion binding|ligand-regulated transcription factor activity|protein dimerization activity|protein kinase binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription factor binding|transcription regulatory region DNA binding			ovary(1)|lung(1)|breast(1)|central_nervous_system(1)	4		all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135)		BRCA - Breast invasive adenocarcinoma(366;0.139)										Hyperimmunoglobulin_E_Recurrent_Infection_Syndrome				---	---	---	---
ATP6V0A1	535	broad.mit.edu	37	17	40623141	40623141	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40623141delA	uc002hzr.2	+						ATP6V0A1_uc002hzq.2_Intron|ATP6V0A1_uc002hzs.2_Intron|ATP6V0A1_uc010wgj.1_Intron|ATP6V0A1_uc010wgk.1_Intron|ATP6V0A1_uc010cyg.2_Intron|ATP6V0A1_uc010wgl.1_Intron	NM_001130021	NP_001123493			ATPase, H+ transporting, lysosomal V0 subunit a1						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytoplasmic vesicle membrane|endosome membrane|Golgi apparatus|integral to membrane|melanosome|nucleus|plasma membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	ATPase binding|hydrogen ion transmembrane transporter activity			pancreas(1)	1		all_cancers(22;1.18e-05)|Breast(137;0.000105)|all_epithelial(22;0.000254)		BRCA - Breast invasive adenocarcinoma(366;0.137)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	40708031	40708034	+	5'Flank	DEL	AAGA	-	-	rs139366873		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40708031_40708034delAAGA	uc002hzy.2	-											Homo sapiens cDNA FLJ32461 fis, clone SKNMC1000168.																														---	---	---	---
CNTNAP1	8506	broad.mit.edu	37	17	40836955	40836955	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40836955delA	uc002iay.2	+						CNTNAP1_uc010wgs.1_Intron	NM_003632	NP_003623			contactin associated protein 1 precursor						axon guidance|cell adhesion	paranode region of axon	receptor activity|receptor binding|SH3 domain binding|SH3/SH2 adaptor activity			ovary(3)|breast(3)|upper_aerodigestive_tract(1)|lung(1)	8		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.143)														---	---	---	---
BRCA1	672	broad.mit.edu	37	17	41264112	41264112	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41264112delT	uc002icq.2	-						BRCA1_uc010whp.1_Intron|BRCA1_uc010whl.1_Intron|BRCA1_uc010whm.1_Intron|BRCA1_uc002icp.3_Intron|BRCA1_uc002icu.2_Intron|BRCA1_uc010cyx.2_Intron|BRCA1_uc002ict.2_Intron|BRCA1_uc010whn.1_Intron|BRCA1_uc010who.1_Intron|BRCA1_uc002idc.1_Intron|BRCA1_uc010whr.1_Intron|BRCA1_uc002idd.2_Intron|BRCA1_uc010cyy.1_Intron|BRCA1_uc010whs.1_Intron|BRCA1_uc010cyz.2_Intron|BRCA1_uc010cza.2_Intron|BRCA1_uc010wht.1_Intron	NM_007294	NP_009225			breast cancer 1, early onset isoform 1						androgen receptor signaling pathway|apoptosis|cellular response to indole-3-methanol|chromosome segregation|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|DNA damage response, signal transduction resulting in induction of apoptosis|double-strand break repair via homologous recombination|fatty acid biosynthetic process|G2/M transition DNA damage checkpoint|negative regulation of centriole replication|negative regulation of fatty acid biosynthetic process|negative regulation of histone H3-K9 methylation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle arrest|positive regulation of DNA repair|positive regulation of histone acetylation|positive regulation of histone H3-K4 methylation|positive regulation of histone H4-K20 methylation|positive regulation of protein ubiquitination|positive regulation of transcription from RNA polymerase II promoter|postreplication repair|protein autoubiquitination|protein K6-linked ubiquitination|regulation of cell motility|regulation of cell proliferation|regulation of transcription from RNA polymerase III promoter|response to estrogen stimulus|response to ionizing radiation|substrate adhesion-dependent cell spreading	BRCA1-A complex|BRCA1-BARD1 complex|gamma-tubulin ring complex|nucleoplasm|plasma membrane|ribonucleoprotein complex|ruffle	androgen receptor binding|identical protein binding|protein binding|RNA binding|transcription coactivator activity|transcription regulatory region DNA binding|tubulin binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(24)|breast(21)|lung(4)|central_nervous_system(1)|endometrium(1)|urinary_tract(1)	52		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)				D|Mis|N|F|S		ovarian	breast|ovarian		Homologous_recombination	Hereditary_Breast-Ovarian_Cancer_BRCA1_type	TCGA Ovarian(2;0.000030)			---	---	---	---
NBR1	4077	broad.mit.edu	37	17	41346969	41346970	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41346969_41346970insT	uc010czd.2	+						NBR1_uc010diz.2_Intron|NBR1_uc010whu.1_Intron|NBR1_uc010whv.1_Intron|NBR1_uc010whw.1_Intron|NBR1_uc010whx.1_3'UTR	NM_031862	NP_114068			neighbor of BRCA1 gene 1						macroautophagy|protein oligomerization	autophagic vacuole|cytoplasmic vesicle|cytosol|late endosome|lysosome|sarcomere	ubiquitin binding|zinc ion binding			skin(1)	1		Breast(137;0.00086)		BRCA - Breast invasive adenocarcinoma(366;0.0934)														---	---	---	---
ETV4	2118	broad.mit.edu	37	17	41606283	41606283	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41606283delT	uc002idw.2	-						ETV4_uc002idv.2_Intron|ETV4_uc010wih.1_Intron|ETV4_uc010czh.2_Intron|ETV4_uc010wii.1_Intron|ETV4_uc002idx.2_Intron|ETV4_uc010wij.1_Intron	NM_001986	NP_001977			ets variant gene 4 (E1A enhancer binding						positive regulation of transcription, DNA-dependent	nucleolus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		EWSR1/ETV4(6)	bone(4)|soft_tissue(2)|ovary(1)	7		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.0798)				T	EWSR1|TMPRSS2|DDX5|KLK2|CANT1	Ewing sarcoma|Prostate carcinoma								---	---	---	---
Unknown	0	broad.mit.edu	37	17	41696401	41696401	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41696401delT								ETV4 (72639 upstream) : MEOX1 (21366 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	41796307	41796309	+	IGR	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41796307_41796309delTTT								MEOX1 (57045 upstream) : SOST (34790 downstream)																																			---	---	---	---
LSM12	124801	broad.mit.edu	37	17	42120464	42120464	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42120464delA	uc002iev.2	-						LSM12_uc010wit.1_Intron|LSM12_uc002iew.1_Intron	NM_152344	NP_689557			LSM12 homolog								protein binding				0		Breast(137;0.0313)|Prostate(33;0.0861)		BRCA - Breast invasive adenocarcinoma(366;0.115)														---	---	---	---
C17orf53	78995	broad.mit.edu	37	17	42229796	42229796	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42229796delA	uc002ifi.1	+						C17orf53_uc010czq.1_Intron|C17orf53_uc002ifj.1_Intron|C17orf53_uc002ifk.1_Intron	NM_024032	NP_076937			hypothetical protein LOC78995												0		Breast(137;0.0364)|Prostate(33;0.0376)		BRCA - Breast invasive adenocarcinoma(366;0.114)														---	---	---	---
FAM171A2	284069	broad.mit.edu	37	17	42443068	42443068	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42443068delT	uc002igs.2	-							NM_198475	NP_940877			family with sequence similarity 171, member A2							integral to membrane					0																		---	---	---	---
GPATCH8	23131	broad.mit.edu	37	17	42490207	42490208	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42490207_42490208delTT	uc002igw.1	-						GPATCH8_uc002igv.1_Intron|GPATCH8_uc010wiz.1_Intron	NM_001002909	NP_001002909			G patch domain containing 8							intracellular	nucleic acid binding|zinc ion binding			ovary(2)|kidney(1)|skin(1)	4		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	42690293	42690294	+	IGR	INS	-	TTTGTTTG	TTTGTTTG	rs143741646	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42690293_42690294insTTTGTTTG								FZD2 (53386 upstream) : C17orf104 (43688 downstream)																																			---	---	---	---
C17orf104	284071	broad.mit.edu	37	17	42731522	42731525	+	5'Flank	DEL	TGTG	-	-	rs10541266		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42731522_42731525delTGTG	uc010czv.2	+							NM_001145080	NP_001138552			hypothetical protein LOC284071											central_nervous_system(1)	1																		---	---	---	---
DBF4B	80174	broad.mit.edu	37	17	42808971	42808971	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42808971delA	uc002ihf.2	+						DBF4B_uc002ihd.1_3'UTR|DBF4B_uc010wjb.1_Intron|DBF4B_uc002ihe.2_Intron|DBF4B_uc010wjc.1_Intron|DBF4B_uc002ihg.2_3'UTR	NM_145663	NP_663696			DBF4 homolog B isoform 1						cell cycle	nucleus	nucleic acid binding|zinc ion binding				0		Prostate(33;0.0322)																---	---	---	---
DBF4B	80174	broad.mit.edu	37	17	42812466	42812466	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42812466delA	uc002ihf.2	+						DBF4B_uc010wjb.1_Intron|DBF4B_uc002ihe.2_Intron|DBF4B_uc010wjc.1_Intron	NM_145663	NP_663696			DBF4 homolog B isoform 1						cell cycle	nucleus	nucleic acid binding|zinc ion binding				0		Prostate(33;0.0322)																---	---	---	---
ACBD4	79777	broad.mit.edu	37	17	43217537	43217538	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43217537_43217538delTT	uc002iid.2	+						ACBD4_uc010wjj.1_Intron|ACBD4_uc002iie.2_Intron|ACBD4_uc002iif.2_Intron|ACBD4_uc002iic.2_Intron|ACBD4_uc010dae.2_Intron	NM_001135707	NP_001129179			acyl-Coenzyme A binding domain containing 4								fatty-acyl-CoA binding			ovary(1)|kidney(1)	2																		---	---	---	---
KIAA1267	284058	broad.mit.edu	37	17	44209494	44209494	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44209494delA	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	44255597	44255598	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44255597_44255598insA	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)																---	---	---	---
WNT3	7473	broad.mit.edu	37	17	44868584	44868584	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44868584delT	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	45237368	45237369	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45237368_45237369delTT	uc002ild.3	-						CDC27_uc002ile.3_Intron|CDC27_uc002ilf.3_Intron|CDC27_uc010wkp.1_Intron|CDC27_uc010wkq.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																		---	---	---	---
KPNB1	3837	broad.mit.edu	37	17	45739476	45739476	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45739476delA	uc002ilt.1	+						KPNB1_uc010wkw.1_Intron|KPNB1_uc010wkx.1_Intron	NM_002265	NP_002256			karyopherin beta 1						DNA fragmentation involved in apoptotic nuclear change|NLS-bearing substrate import into nucleus|protein import into nucleus, translocation|ribosomal protein import into nucleus|viral genome transport in host cell|viral infectious cycle	cytosol|nuclear pore|nucleoplasm	nuclear localization sequence binding|protein domain specific binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
SKAP1	8631	broad.mit.edu	37	17	46214955	46214955	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46214955delT	uc002ini.1	-						SKAP1_uc002inj.1_Intron|SKAP1_uc010dbd.1_Intron|SKAP1_uc010dbe.1_Intron	NM_003726	NP_003717			src kinase associated phosphoprotein 1 isoform						positive regulation of transcription from RNA polymerase II promoter|T cell receptor signaling pathway	cytoplasm|nucleus|plasma membrane	antigen binding|protein kinase binding|SH2 domain binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	46792984	46792984	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46792984delT								MIR196A1 (83063 upstream) : PRAC (6108 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	46819221	46819221	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46819221delT								HOXB13 (13110 upstream) : TTLL6 (20373 downstream)																																			---	---	---	---
SLC35B1	10237	broad.mit.edu	37	17	47780109	47780109	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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	47945188	47945189	+	IGR	INS	-	C	C	rs146650807	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47945188_47945189insC								TAC4 (19809 upstream) : DLX4 (101373 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	48284265	48284266	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48284265_48284266insT								COL1A1 (5265 upstream) : TMEM92 (67571 downstream)																																			---	---	---	---
LUC7L3	51747	broad.mit.edu	37	17	48824390	48824390	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48824390delT	uc002isr.2	+						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																		---	---	---	---
NME1-NME2	654364	broad.mit.edu	37	17	49247504	49247512	+	Intron	DEL	TTTTTTTTT	-	-	rs112707943		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49247504_49247512delTTTTTTTTT	uc002itk.2	+						NME1-NME2_uc002itj.2_Intron|NME2_uc002itl.2_Intron|NME2_uc002itm.2_Intron|NME2_uc002itn.2_Intron|NME2_uc002ito.2_Intron	NM_002512	NP_002503			nucleoside diphosphate kinase B						cell adhesion|CTP biosynthetic process|GTP biosynthetic process|negative regulation of apoptosis|nucleobase, nucleoside and nucleotide interconversion|positive regulation of epithelial cell proliferation|positive regulation of keratinocyte differentiation|UTP biosynthetic process	cytosol|lamellipodium|nucleus|ruffle	ATP binding|DNA binding|metal ion binding|nucleoside diphosphate kinase activity|protein binding|protein histidine kinase activity|sequence-specific DNA binding transcription factor activity				0			BRCA - Breast invasive adenocarcinoma(22;1.54e-08)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	49578932	49578932	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49578932delT								UTP18 (203642 upstream) : CA10 (128743 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	49586242	49586242	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49586242delA								UTP18 (210952 upstream) : CA10 (121433 downstream)																																			---	---	---	---
CA10	56934	broad.mit.edu	37	17	49896889	49896890	+	Intron	DEL	CA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49896889_49896890delCA	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	50262479	50262479	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50262479delT								CA10 (25102 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	50621522	50621522	+	IGR	DEL	T	-	-	rs113478162		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50621522delT								CA10 (384145 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	51965736	51965736	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51965736delA								KIF2B (63163 upstream) : None (None downstream)																																			---	---	---	---
ANKFN1	162282	broad.mit.edu	37	17	54403876	54403877	+	Intron	DEL	CA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54403876_54403877delCA	uc002iun.1	+							NM_153228	NP_694960			ankyrin-repeat and fibronectin type III domain											large_intestine(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	54712979	54712980	+	IGR	INS	-	GATAGATAGATA	GATAGATAGATA	rs140392654	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54712979_54712980insGATAGATAGATA								NOG (40028 upstream) : C17orf67 (156295 downstream)																																			---	---	---	---
SCPEP1	59342	broad.mit.edu	37	17	55061191	55061191	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55061191delT	uc002iuv.3	+						SCPEP1_uc010dcl.2_Intron|SCPEP1_uc010wnk.1_Intron	NM_021626	NP_067639			serine carboxypeptidase 1 precursor						proteolysis	extracellular region	serine-type carboxypeptidase activity			skin(1)	1	Breast(9;2.86e-08)																	---	---	---	---
Unknown	0	broad.mit.edu	37	17	55318194	55318196	+	IGR	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55318194_55318196delAAA								AKAP1 (119485 upstream) : MSI2 (15016 downstream)																																			---	---	---	---
MSI2	124540	broad.mit.edu	37	17	55663709	55663710	+	Intron	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55663709_55663710delTC	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	55693643	55693644	+	Intron	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55693643_55693644delTG	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								---	---	---	---
RNF43	54894	broad.mit.edu	37	17	56446430	56446433	+	Intron	DEL	ACAC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56446430_56446433delACAC	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)																	---	---	---	---
RAD51C	5889	broad.mit.edu	37	17	56801800	56801801	+	Intron	DEL	AA	-	-	rs113719550		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56801800_56801801delAA	uc002iwu.2	+						RAD51C_uc010woa.1_Intron|RAD51C_uc010ddc.2_Intron|RAD51C_uc002iwv.2_Intron|RAD51C_uc002iww.2_Intron	NM_058216	NP_478123			RAD51 homolog C isoform 1						blood coagulation|DNA repair	mitochondrion|nucleoplasm|perinuclear region of cytoplasm	ATP binding|DNA binding|DNA-dependent ATPase activity				0	Medulloblastoma(34;0.127)|all_neural(34;0.237)												Homologous_recombination	Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2				---	---	---	---
TRIM37	4591	broad.mit.edu	37	17	57082653	57082653	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57082653delT	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				---	---	---	---
TRIM37	4591	broad.mit.edu	37	17	57139823	57139823	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57139823delA	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				---	---	---	---
SKA2	348235	broad.mit.edu	37	17	57220575	57220575	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57220575delT	uc002ixd.2	-						SKA2_uc010dde.1_Intron|SKA2_uc002ixe.2_Intron	NM_182620	NP_872426			spindle and KT associated 2 isoform 1						cell division|chromosome segregation|mitotic anaphase|mitotic prometaphase|regulation of microtubule polymerization or depolymerization	condensed chromosome outer kinetochore|cytosol|spindle microtubule	microtubule binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	57687463	57687463	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57687463delT								DHX40 (1761 upstream) : CLTC (9587 downstream)																																			---	---	---	---
USP32	84669	broad.mit.edu	37	17	58447113	58447113	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58447113delT	uc002iyo.1	-						USP32_uc010wov.1_Intron	NM_032582	NP_115971			ubiquitin specific protease 32						protein deubiquitination|ubiquitin-dependent protein catabolic process	Golgi apparatus|membrane	calcium ion binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|breast(2)|large_intestine(1)	5	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)															---	---	---	---
USP32	84669	broad.mit.edu	37	17	58458057	58458058	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58458057_58458058insA	uc002iyo.1	-						USP32_uc010wov.1_Intron	NM_032582	NP_115971			ubiquitin specific protease 32						protein deubiquitination|ubiquitin-dependent protein catabolic process	Golgi apparatus|membrane	calcium ion binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|breast(2)|large_intestine(1)	5	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	58609725	58609725	+	IGR	DEL	A	-	-	rs115206478	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58609725delA								APPBP2 (6145 upstream) : PPM1D (67829 downstream)																																			---	---	---	---
BCAS3	54828	broad.mit.edu	37	17	58952111	58952111	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58952111delT	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	59365106	59365106	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59365106delA	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)															---	---	---	---
TBX4	9496	broad.mit.edu	37	17	59536278	59536278	+	Intron	DEL	G	-	-	rs113580135		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59536278delG	uc002izi.2	+						TBX4_uc010ddo.2_Intron|TBX4_uc010woy.1_Intron	NM_018488	NP_060958			T-box 4						leg morphogenesis|skeletal system morphogenesis	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			skin(2)	2																		---	---	---	---
INTS2	57508	broad.mit.edu	37	17	59974795	59974796	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59974795_59974796delTT	uc002izn.2	-						INTS2_uc002izm.2_Intron	NM_020748	NP_065799			integrator complex subunit 2						snRNA processing	integral to membrane|integrator complex|nuclear membrane	protein binding			ovary(1)|lung(1)|pancreas(1)	3																		---	---	---	---
TLK2	11011	broad.mit.edu	37	17	60559815	60559816	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60559815_60559816delTT	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																		---	---	---	---
TLK2	11011	broad.mit.edu	37	17	60572529	60572529	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60572529delA	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																		---	---	---	---
TLK2	11011	broad.mit.edu	37	17	60574455	60574455	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60574455delA	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																		---	---	---	---
TLK2	11011	broad.mit.edu	37	17	60607190	60607190	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60607190delT	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																		---	---	---	---
TLK2	11011	broad.mit.edu	37	17	60675891	60675892	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60675891_60675892delTT	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																		---	---	---	---
MRC2	9902	broad.mit.edu	37	17	60738676	60738676	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60738676delT	uc002jad.2	+						MRC2_uc002jac.2_Intron	NM_006039	NP_006030			mannose receptor, C type 2						endocytosis	integral to membrane	receptor activity|sugar binding			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
MIR633	693218	broad.mit.edu	37	17	61021673	61021673	+	RNA	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61021673delA	hsa-mir-633|MI0003648	+			c.98delA																				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	61058723	61058723	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61058723delC								MIR633 (37050 upstream) : TANC2 (28175 downstream)																																			---	---	---	---
TANC2	26115	broad.mit.edu	37	17	61085918	61085918	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61085918delT	uc002jal.3	+							NM_025185	NP_079461			tetratricopeptide repeat, ankyrin repeat and								binding			ovary(2)	2																		---	---	---	---
TANC2	26115	broad.mit.edu	37	17	61435714	61435717	+	Intron	DEL	GAGA	-	-	rs5821386		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61435714_61435717delGAGA	uc002jal.3	+						TANC2_uc010wpe.1_Intron|TANC2_uc002jam.1_Intron	NM_025185	NP_079461			tetratricopeptide repeat, ankyrin repeat and								binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	61982146	61982146	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61982146delT								CSH2 (8159 upstream) : CSHL1 (4819 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	63397318	63397318	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63397318delT								RGS9 (173499 upstream) : AXIN2 (127367 downstream)																																			---	---	---	---
AXIN2	8313	broad.mit.edu	37	17	63532780	63532780	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63532780delA	uc002jfi.2	-						AXIN2_uc002jfh.2_Intron	NM_004655	NP_004646			axin 2						cellular protein localization|cellular response to organic cyclic compound|dorsal/ventral axis specification|intramembranous ossification|maintenance of DNA repeat elements|mRNA stabilization|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of cell proliferation|negative regulation of osteoblast differentiation|odontogenesis|positive regulation of cell death|positive regulation of epithelial to mesenchymal transition|positive regulation of protein phosphorylation|regulation of centromeric sister chromatid cohesion|regulation of mismatch repair|Wnt receptor signaling pathway involved in somitogenesis	Axin-APC-beta-catenin-GSK3B complex|cell cortex|centrosome|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|nucleus|plasma membrane|postsynaptic density	armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding			central_nervous_system(1)|skin(1)	2														Oligodontia_Ectodermal_Dysplasia_and_Colorectal_Polyp_syndrome				---	---	---	---
CCDC46	201134	broad.mit.edu	37	17	63749783	63749783	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63749783delT	uc002jfl.2	-						CCDC46_uc010deo.2_Intron|CCDC46_uc002jfm.2_Intron|CCDC46_uc010dep.2_Intron|CCDC46_uc002jfk.2_Intron	NM_145036	NP_659473			coiled-coil domain containing 46 isoform a							centrosome					0			BRCA - Breast invasive adenocarcinoma(6;1.53e-06)															---	---	---	---
CCDC46	201134	broad.mit.edu	37	17	64002046	64002047	+	Intron	INS	-	ATACT	ATACT	rs144597978	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64002046_64002047insATACT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	64262149	64262149	+	IGR	DEL	T	-	-	rs66508147		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64262149delT								APOH (36593 upstream) : PRKCA (36777 downstream)																																			---	---	---	---
PRKCA	5578	broad.mit.edu	37	17	64774884	64774884	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64774884delG	uc002jfp.1	+							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)													---	---	---	---
NOL11	25926	broad.mit.edu	37	17	65722457	65722457	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65722457delT	uc002jgd.1	+						NOL11_uc010wql.1_Intron|NOL11_uc010deu.1_Intron	NM_015462	NP_056277			nucleolar protein 11							nucleolus					0	all_cancers(12;1.54e-10)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0518)|COAD - Colon adenocarcinoma(4;0.0977)|LUSC - Lung squamous cell carcinoma(166;0.24)															---	---	---	---
NOL11	25926	broad.mit.edu	37	17	65732201	65732202	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65732201_65732202delAC	uc002jgd.1	+						NOL11_uc010wql.1_Intron|NOL11_uc010deu.1_Intron	NM_015462	NP_056277			nucleolar protein 11							nucleolus					0	all_cancers(12;1.54e-10)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0518)|COAD - Colon adenocarcinoma(4;0.0977)|LUSC - Lung squamous cell carcinoma(166;0.24)															---	---	---	---
KPNA2	3838	broad.mit.edu	37	17	66033402	66033402	+	Intron	DEL	A	-	-	rs34040105		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66033402delA	uc002jgk.2	+						KPNA2_uc002jgl.2_Intron	NM_002266	NP_002257			karyopherin alpha 2						DNA metabolic process|G2 phase of mitotic cell cycle|interspecies interaction between organisms|M phase specific microtubule process|NLS-bearing substrate import into nucleus|regulation of DNA recombination	cytoplasm|nuclear pore|nucleoplasm	histone deacetylase binding|nuclear localization sequence binding|protein transporter activity			central_nervous_system(2)	2	all_cancers(12;1.18e-09)		BRCA - Breast invasive adenocarcinoma(8;1.03e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	66230929	66230930	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66230929_66230930delAA								LOC440461 (34493 upstream) : AMZ2 (13215 downstream)																																			---	---	---	---
ARSG	22901	broad.mit.edu	37	17	66376394	66376394	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66376394delT	uc002jhc.2	+						ARSG_uc002jhb.1_Intron	NM_014960	NP_055775			Arylsulfatase G precursor						sulfur compound metabolic process	endoplasmic reticulum|extracellular space|lysosome	arylsulfatase activity|metal ion binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	66482343	66482344	+	IGR	DEL	TT	-	-	rs34725091		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66482343_66482344delTT								WIPI1 (28690 upstream) : PRKAR1A (25766 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	66484123	66484124	+	IGR	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66484123_66484124delAG								WIPI1 (30470 upstream) : PRKAR1A (23986 downstream)																																			---	---	---	---
ABCA8	10351	broad.mit.edu	37	17	66872446	66872446	+	Intron	DEL	T	-	-	rs4148026		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66872446delT	uc002jhp.2	-						ABCA8_uc002jhq.2_Intron|ABCA8_uc010wqq.1_Intron	NM_007168	NP_009099			ATP-binding cassette, sub-family A member 8							integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3	Breast(10;4.56e-13)																	---	---	---	---
ABCA6	23460	broad.mit.edu	37	17	67100707	67100707	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67100707delT	uc002jhw.1	-							NM_080284	NP_525023			ATP-binding cassette, sub-family A, member 6						transport	integral to membrane	ATP binding|ATPase activity			upper_aerodigestive_tract(2)|large_intestine(2)|ovary(2)|skin(1)	7	Breast(10;5.65e-12)																	---	---	---	---
Unknown	0	broad.mit.edu	37	17	68350640	68350640	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68350640delT								KCNJ2 (174459 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	68917358	68917359	+	IGR	INS	-	TG	TG	rs34413452		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68917358_68917359insTG								KCNJ2 (741177 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	69088895	69088895	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69088895delT								KCNJ2 (912714 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	69163511	69163511	+	Intron	DEL	A	-	-	rs34443060		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69163511delA	uc002jis.3	-											Homo sapiens cDNA clone IMAGE:5267277.																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	69205741	69205741	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69205741delT								None (None upstream) : SOX9 (911420 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	69263574	69263575	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69263574_69263575insA								None (None upstream) : SOX9 (853586 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	69936060	69936060	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69936060delT								None (None upstream) : SOX9 (181101 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	70275267	70275267	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70275267delT								SOX9 (152715 upstream) : SLC39A11 (366819 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	70489724	70489724	+	Intron	DEL	T	-	-	rs5821914		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70489724delT	uc002jix.2	-						uc002jiz.1_Intron					Homo sapiens cDNA FLJ20470 fis, clone KAT06815.																														---	---	---	---
SLC39A11	201266	broad.mit.edu	37	17	70812535	70812535	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70812535delA	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																		---	---	---	---
SDK2	54549	broad.mit.edu	37	17	71370611	71370612	+	Intron	DEL	TT	-	-	rs113491998		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71370611_71370612delTT	uc010dfm.2	-						SDK2_uc002jjt.3_Intron|SDK2_uc010dfn.2_Intron	NM_001144952	NP_001138424			sidekick 2						cell adhesion	integral to membrane				ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	71729455	71729456	+	IGR	INS	-	T	T	rs143300916	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71729455_71729456insT								SDK2 (89228 upstream) : C17orf54 (15953 downstream)																																			---	---	---	---
CD300LB	124599	broad.mit.edu	37	17	72518441	72518441	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72518441delA	uc002jkx.2	-	4						NM_174892	NP_777552			CD300 molecule-like family member b							integral to membrane|plasma membrane	receptor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	72642126	72642126	+	IGR	DEL	A	-	-	rs34327039		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72642126delA								CD300E (22325 upstream) : RAB37 (25130 downstream)																																			---	---	---	---
GRB2	2885	broad.mit.edu	37	17	73326789	73326791	+	Intron	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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	73376839	73376840	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73376839_73376840insA	uc002jnx.3	-						GRB2_uc002jny.3_Intron	NM_002086	NP_002077			growth factor receptor-bound protein 2 isoform						axon guidance|blood coagulation|cell junction assembly|cell-cell signaling|cellular response to ionizing radiation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of reactive oxygen species metabolic process|Ras protein signal transduction|receptor internalization|signal transduction in response to DNA damage|T cell costimulation	cytosol|Golgi apparatus	epidermal growth factor receptor binding|insulin receptor substrate binding|SH3/SH2 adaptor activity			ovary(3)	3	all_cancers(13;5.44e-09)|all_epithelial(9;1.1e-09)|Breast(9;1.85e-09)|all_lung(278;0.222)		all cancers(21;1.09e-07)|Epithelial(20;1.23e-06)|Lung(188;0.185)		Pegademase bovine(DB00061)													---	---	---	---
LLGL2	3993	broad.mit.edu	37	17	73523857	73523858	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73523857_73523858delTT	uc002joh.2	+						LLGL2_uc002jog.1_Intron|LLGL2_uc010dgf.1_Intron|LLGL2_uc002joi.2_Intron	NM_001031803	NP_001026973			lethal giant larvae homolog 2 isoform c						cell cycle|cell division|exocytosis|regulation of establishment or maintenance of cell polarity	cytoplasm|intracellular membrane-bounded organelle	PDZ domain binding			ovary(2)	2	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)															---	---	---	---
SRP68	6730	broad.mit.edu	37	17	74064537	74064540	+	Intron	DEL	AAAA	-	-	rs113014100		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74064537_74064540delAAAA	uc002jqk.1	-						SRP68_uc010wsu.1_Intron|SRP68_uc002jql.1_Intron	NM_014230	NP_055045			signal recognition particle 68kDa						response to drug	cytosol|endoplasmic reticulum|nucleolus|ribosome|signal recognition particle, endoplasmic reticulum targeting	RNA binding|signal recognition particle binding			ovary(1)	1																		---	---	---	---
RNF157	114804	broad.mit.edu	37	17	74162632	74162632	+	Intron	DEL	A	-	-	rs67444473		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74162632delA	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	74174907	74174907	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74174907delT	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	74315558	74315558	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74315558delT	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	74500716	74500717	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74500716_74500717insT								RHBDF2 (3208 upstream) : CYGB (22723 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	74585548	74585550	+	IGR	DEL	CTC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74585548_74585550delCTC								ST6GALNAC2 (3403 upstream) : ST6GALNAC1 (35297 downstream)																																			---	---	---	---
SEPT9	10801	broad.mit.edu	37	17	75335597	75335597	+	Intron	DEL	T	-	-	rs34622485		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75335597delT	uc002jts.3	+						SEPT9_uc010wtk.1_Intron|SEPT9_uc002jtt.3_Intron|SEPT9_uc002jtu.3_Intron	NM_001113491	NP_001106963			septin 9 isoform a						cell cycle|cell division|protein heterooligomerization	microtubule|perinuclear region of cytoplasm|stress fiber	GTP binding|GTPase activity|protein binding|protein binding			breast(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(99;0.153)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	75921980	75921987	+	IGR	DEL	AAGGAAGA	-	-	rs67051242		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75921980_75921987delAAGGAAGA								FLJ45079 (41811 upstream) : TNRC6C (78331 downstream)																																			---	---	---	---
LOC283999	283999	broad.mit.edu	37	17	76232904	76232904	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76232904delG	uc002jvk.2	+						LOC283999_uc010dhm.1_Intron	NM_001145529	NP_001139001			hypothetical protein LOC283999							integral to membrane|tight junction	structural molecule activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	76341206	76341207	+	IGR	INS	-	C	C	rs138009981	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76341206_76341207insC								LOC283999 (104139 upstream) : SOCS3 (11652 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	76473002	76473003	+	IGR	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76473002_76473003delGT								DNAH17 (4146 upstream) : CYTH1 (197128 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	76611979	76611980	+	IGR	INS	-	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76611979_76611980insG								DNAH17 (143123 upstream) : CYTH1 (58151 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	77718129	77718130	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77718129_77718130delTT								ENPP7 (2109 upstream) : CBX2 (33863 downstream)																																			---	---	---	---
TBC1D16	125058	broad.mit.edu	37	17	77956490	77956490	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77956490delA	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)															---	---	---	---
CARD14	79092	broad.mit.edu	37	17	78177069	78177071	+	Intron	DEL	AAA	-	-	rs5822329		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78177069_78177071delAAA	uc002jxw.1	+						CARD14_uc002jxt.1_Intron|CARD14_uc010wud.1_Intron	NM_024110	NP_077015			caspase recruitment domain protein 14 isoform 1						activation of NF-kappaB-inducing kinase activity|positive regulation of protein phosphorylation|regulation of apoptosis	aggresome|cytoplasm|plasma membrane	CARD domain binding			ovary(4)|skin(1)	5	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.017)|BRCA - Breast invasive adenocarcinoma(99;0.0908)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	78484460	78484461	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78484460_78484461insT								NPTX1 (34056 upstream) : RPTOR (34164 downstream)																																			---	---	---	---
LOC388428	388428	broad.mit.edu	37	17	79151364	79151364	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79151364delA	uc010wuk.1	+						LOC388428_uc010wul.1_Intron					SubName: Full=cDNA FLJ44861 fis, clone BRALZ2008930;												0																		---	---	---	---
NPLOC4	55666	broad.mit.edu	37	17	79528009	79528009	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79528009delT	uc002kat.3	-						NPLOC4_uc002kar.2_RNA|NPLOC4_uc010dic.2_Intron|NPLOC4_uc002kas.2_Intron	NM_017921	NP_060391			nuclear protein localization 4						cellular membrane fusion|ER-associated protein catabolic process|Golgi organization	cytosol|endoplasmic reticulum|nuclear outer membrane-endoplasmic reticulum membrane network|nucleus	zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_neural(118;0.0878)|Melanoma(429;0.242)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)															---	---	---	---
ASPSCR1	79058	broad.mit.edu	37	17	79951075	79951075	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79951075delT	uc002kcx.2	+						ASPSCR1_uc002kcw.1_Intron|ASPSCR1_uc002kcy.2_Intron|ASPSCR1_uc002kcz.2_Intron|ASPSCR1_uc002kda.2_Intron|ASPSCR1_uc002kdb.1_Intron	NM_024083	NP_076988			alveolar soft part sarcoma chromosome region,								protein binding		ASPSCR1/TFE3(161)	soft_tissue(118)|kidney(43)|breast(1)	162	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)					T	TFE3	alveolar soft part sarcoma								---	---	---	---
FOXK2	3607	broad.mit.edu	37	17	80498156	80498157	+	Intron	DEL	AA	-	-	rs112333610		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80498156_80498157delAA	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	80774418	80774418	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80774418delT	uc002kfz.2	+						TBCD_uc002kfx.1_Intron|TBCD_uc002kfy.1_Intron	NM_005993	NP_005984			beta-tubulin cofactor D						'de novo' posttranslational protein folding|adherens junction assembly|negative regulation of cell-substrate adhesion|negative regulation of microtubule polymerization|post-chaperonin tubulin folding pathway|tight junction assembly	adherens junction|cytoplasm|lateral plasma membrane|microtubule|tight junction	beta-tubulin binding|chaperone binding|GTPase activator activity				0	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)															---	---	---	---
TBCD	6904	broad.mit.edu	37	17	80878978	80878978	+	Intron	DEL	T	-	-	rs3214867		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80878978delT	uc002kfz.2	+						TBCD_uc002kfx.1_Intron|TBCD_uc002kfy.1_Intron|TBCD_uc002kgb.1_Intron	NM_005993	NP_005984			beta-tubulin cofactor D						'de novo' posttranslational protein folding|adherens junction assembly|negative regulation of cell-substrate adhesion|negative regulation of microtubule polymerization|post-chaperonin tubulin folding pathway|tight junction assembly	adherens junction|cytoplasm|lateral plasma membrane|microtubule|tight junction	beta-tubulin binding|chaperone binding|GTPase activator activity				0	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)															---	---	---	---
B3GNTL1	146712	broad.mit.edu	37	17	80903812	80903812	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80903812delT	uc002kgg.1	-						B3GNTL1_uc002kgf.1_Intron|B3GNTL1_uc002kge.1_Intron	NM_001009905	NP_001009905			UDP-GlcNAc:betaGal								transferase activity, transferring glycosyl groups			ovary(1)|pancreas(1)	2	Breast(20;0.000443)|all_neural(118;0.0779)	all_cancers(8;0.0396)|all_epithelial(8;0.0556)	BRCA - Breast invasive adenocarcinoma(99;0.0517)|OV - Ovarian serous cystadenocarcinoma(97;0.0868)															---	---	---	---
B3GNTL1	146712	broad.mit.edu	37	17	80957818	80957818	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80957818delT	uc002kgg.1	-						B3GNTL1_uc002kgf.1_Intron|B3GNTL1_uc002kge.1_Intron	NM_001009905	NP_001009905			UDP-GlcNAc:betaGal								transferase activity, transferring glycosyl groups			ovary(1)|pancreas(1)	2	Breast(20;0.000443)|all_neural(118;0.0779)	all_cancers(8;0.0396)|all_epithelial(8;0.0556)	BRCA - Breast invasive adenocarcinoma(99;0.0517)|OV - Ovarian serous cystadenocarcinoma(97;0.0868)															---	---	---	---
B3GNTL1	146712	broad.mit.edu	37	17	81011517	81011517	+	5'Flank	DEL	T	-	-	rs71376547		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:81011517delT	uc002kgg.1	-							NM_001009905	NP_001009905			UDP-GlcNAc:betaGal								transferase activity, transferring glycosyl groups			ovary(1)|pancreas(1)	2	Breast(20;0.000443)|all_neural(118;0.0779)	all_cancers(8;0.0396)|all_epithelial(8;0.0556)	BRCA - Breast invasive adenocarcinoma(99;0.0517)|OV - Ovarian serous cystadenocarcinoma(97;0.0868)															---	---	---	---
THOC1	9984	broad.mit.edu	37	18	226749	226749	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:226749delT	uc002kkj.3	-						THOC1_uc002kkk.3_Intron|THOC1_uc002kkl.2_Intron|THOC1_uc002kkh.3_5'Flank	NM_005131	NP_005122			THO complex 1						apoptosis|intronless viral mRNA export from host nucleus|mRNA processing|regulation of transcription elongation, DNA-dependent|RNA splicing|signal transduction|transcription, DNA-dependent	cytoplasm|nuclear matrix|nuclear speck|THO complex part of transcription export complex	DNA binding|protein binding|RNA binding			ovary(1)	1		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)																---	---	---	---
COLEC12	81035	broad.mit.edu	37	18	440150	440150	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:440150delA	uc002kkm.2	-							NM_130386	NP_569057			collectin sub-family member 12						carbohydrate mediated signaling|innate immune response|phagocytosis, recognition|protein homooligomerization	collagen|integral to membrane	galactose binding|low-density lipoprotein particle binding|metal ion binding|pattern recognition receptor activity|scavenger receptor activity			ovary(1)|pancreas(1)	2		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	1153520	1153522	+	IGR	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:1153520_1153522delTTT								ADCYAP1 (241349 upstream) : C18orf2 (100868 downstream)																																			---	---	---	---
C18orf2	56651	broad.mit.edu	37	18	1310438	1310438	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:1310438delA	uc002klb.1	-						C18orf2_uc002klg.2_Intron|C18orf2_uc002klc.1_Intron|C18orf2_uc010dki.1_Intron|C18orf2_uc002kld.1_Intron|C18orf2_uc002kle.1_Intron|C18orf2_uc002klf.1_Intron					Homo sapiens C18orf2 isoform 1 mRNA, complete sequence, alternatively spliced.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	2217177	2217177	+	IGR	DEL	A	-	-	rs78857598		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2217177delA								C18orf2 (809996 upstream) : METTL4 (320348 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	2413422	2413422	+	IGR	DEL	A	-	-	rs79228797	byFrequency;by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2413422delA								None (None upstream) : METTL4 (124103 downstream)																																			---	---	---	---
METTL4	64863	broad.mit.edu	37	18	2565278	2565278	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2565278delA	uc002klh.3	-							NM_022840	NP_073751			methyltransferase like 4						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		methyltransferase activity|nucleic acid binding			kidney(1)|skin(1)	2																		---	---	---	---
SMCHD1	23347	broad.mit.edu	37	18	2705663	2705664	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2705663_2705664delTT	uc002klm.3	+						SMCHD1_uc002klk.3_Intron|SMCHD1_uc002kll.3_5'Flank	NM_015295	NP_056110			structural maintenance of chromosomes flexible						chromosome organization		ATP binding				0																		---	---	---	---
MYOM1	8736	broad.mit.edu	37	18	3094390	3094393	+	Intron	DEL	AAAC	-	-	rs71159041		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3094390_3094393delAAAC	uc002klp.2	-						MYOM1_uc002klq.2_Intron	NM_003803	NP_003794			myomesin 1 isoform a							striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	3475727	3475728	+	Intron	DEL	AA	-	-	rs79067037		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3475727_3475728delAA	uc002kmd.1	+											Sequence 153 from Patent WO0220754.																														---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	4128899	4128899	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4128899delT	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	4601727	4601728	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4601727_4601728insT								DLGAP1 (146461 upstream) : LOC642597 (541944 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	4912863	4912864	+	IGR	INS	-	TTC	TTC	rs143287953	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4912863_4912864insTTC								DLGAP1 (457597 upstream) : LOC642597 (230808 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	5247374	5247374	+	IGR	DEL	T	-	-	rs36050885		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5247374delT								LOC339290 (871 upstream) : ZFP161 (41645 downstream)																																			---	---	---	---
EPB41L3	23136	broad.mit.edu	37	18	5410217	5410217	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5410217delA	uc002kmt.1	-						EPB41L3_uc010wzh.1_Intron|EPB41L3_uc002kmu.1_Intron|EPB41L3_uc010dkq.1_Intron|EPB41L3_uc002kms.1_Intron|EPB41L3_uc010wze.1_Intron|EPB41L3_uc010wzf.1_Intron|EPB41L3_uc010wzg.1_Intron|EPB41L3_uc010dkr.2_Intron	NM_012307	NP_036439			erythrocyte membrane protein band 4.1-like 3						cortical actin cytoskeleton organization	cell-cell junction|cytoplasm|cytoskeleton|extrinsic to membrane	actin binding|structural molecule activity			ovary(5)	5																		---	---	---	---
L3MBTL4	91133	broad.mit.edu	37	18	6285482	6285483	+	Intron	INS	-	GT	GT	rs146666645	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6285482_6285483insGT	uc002kmz.3	-						L3MBTL4_uc010dkt.2_Intron	NM_173464	NP_775735			l(3)mbt-like 4						chromatin modification	nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|pancreas(1)	3		Colorectal(10;0.0249)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	6782110	6782110	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6782110delT								L3MBTL4 (367200 upstream) : ARHGAP28 (6383 downstream)																																			---	---	---	---
ARHGAP28	79822	broad.mit.edu	37	18	6819147	6819147	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6819147delT	uc002knc.2	+							NM_030672	NP_109597			Rho GTPase activating protein 28 isoform b						signal transduction	intracellular				pancreas(1)	1		Colorectal(10;0.168)																---	---	---	---
ARHGAP28	79822	broad.mit.edu	37	18	6894738	6894738	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6894738delA	uc010wzi.1	+						ARHGAP28_uc002knc.2_Intron|ARHGAP28_uc002knd.2_Intron|ARHGAP28_uc002kne.2_Intron|ARHGAP28_uc002knf.2_Intron					SubName: Full=Putative uncharacterized protein ARHGAP28;						signal transduction	intracellular				pancreas(1)	1		Colorectal(10;0.168)																---	---	---	---
PTPRM	5797	broad.mit.edu	37	18	7918077	7918082	+	Intron	DEL	TGTGTG	-	-	rs56699123		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7918077_7918082delTGTGTG	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	8497230	8497232	+	IGR	DEL	TTT	-	-	rs112532764		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8497230_8497232delTTT								PTPRM (90372 upstream) : RAB12 (112203 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	8930212	8930213	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8930212_8930213delAA								KIAA0802 (97437 upstream) : NDUFV2 (172462 downstream)																																			---	---	---	---
ANKRD12	23253	broad.mit.edu	37	18	9159801	9159801	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9159801delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	9293579	9293579	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9293579delT								ANKRD12 (8373 upstream) : TWSG1 (41186 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	9301391	9301394	+	IGR	DEL	ACAG	-	-	rs72024558		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9301391_9301394delACAG								ANKRD12 (16185 upstream) : TWSG1 (33371 downstream)																																			---	---	---	---
PPP4R1	9989	broad.mit.edu	37	18	9594801	9594801	+	Intron	DEL	T	-	-	rs77692629		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9594801delT	uc002koe.1	-						PPP4R1_uc010wzo.1_Intron|PPP4R1_uc002kod.1_Intron|PPP4R1_uc010wzp.1_Intron	NM_001042388	NP_001035847			protein phosphatase 4, regulatory subunit 1						protein phosphorylation|signal transduction	protein phosphatase 4 complex	protein binding|protein phosphatase type 4 regulator activity			skin(1)	1																		---	---	---	---
RAB31	11031	broad.mit.edu	37	18	9726918	9726918	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9726918delA	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																		---	---	---	---
FAM38B	63895	broad.mit.edu	37	18	10874470	10874470	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10874470delA	uc002kow.1	-											RecName: Full=Uncharacterized protein C18orf58;							integral to membrane	ion channel activity			ovary(1)	1																		---	---	---	---
GNAL	2774	broad.mit.edu	37	18	11823340	11823340	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11823340delT	uc010dkz.2	+						GNAL_uc002kqc.2_Intron|GNAL_uc002kqd.2_Intron	NM_001142339	NP_001135811			guanine nucleotide binding protein (G protein),						activation of adenylate cyclase activity by dopamine receptor signaling pathway|inhibition of adenylate cyclase activity by G-protein signaling pathway|sensory perception of smell|synaptic transmission	heterotrimeric G-protein complex	adenylate cyclase activity|G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)	1																		---	---	---	---
AFG3L2	10939	broad.mit.edu	37	18	12337293	12337293	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12337293delT	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)													---	---	---	---
PTPN2	5771	broad.mit.edu	37	18	12847047	12847048	+	Intron	INS	-	A	A	rs111911973		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12847047_12847048insA	uc002krp.2	-						PTPN2_uc002krl.2_Intron|PTPN2_uc002krn.2_Intron|PTPN2_uc002kro.2_Intron|PTPN2_uc002krm.2_Intron	NM_002828	NP_002819			protein tyrosine phosphatase, non-receptor type						interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway	endoplasmic reticulum|nucleoplasm	protein binding			skin(2)	2		Lung NSC(161;8.94e-06)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	13200455	13200456	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13200455_13200456delTT								CEP192 (75406 upstream) : C18orf1 (18330 downstream)																																			---	---	---	---
C18orf1	753	broad.mit.edu	37	18	13315966	13315967	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13315966_13315967insA	uc002ksa.2	+						C18orf1_uc002ksb.2_Intron	NM_181481	NP_852146			hypothetical protein LOC753 isoform alpha 1							integral to membrane|plasma membrane				ovary(2)|skin(1)	3				READ - Rectum adenocarcinoma(73;0.0642)														---	---	---	---
C18orf1	753	broad.mit.edu	37	18	13536609	13536609	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13536609delT	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)														---	---	---	---
RNMT	8731	broad.mit.edu	37	18	13742794	13742795	+	Intron	DEL	AA	-	-	rs7229786		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13742794_13742795delAA	uc002ksk.1	+						RNMT_uc002ksl.1_Intron|RNMT_uc002ksm.1_Intron|RNMT_uc010dlk.2_Intron|RNMT_uc010xae.1_Intron	NM_003799	NP_003790			RNA (guanine-7-) methyltransferase						mRNA capping|transcription from RNA polymerase II promoter|viral reproduction	nucleoplasm	mRNA (guanine-N7-)-methyltransferase activity|RNA binding				0																		---	---	---	---
ZNF519	162655	broad.mit.edu	37	18	14117175	14117175	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14117175delA	uc002kst.1	-						ZNF519_uc002ksq.1_Intron|ZNF519_uc002ksr.1_Intron|ZNF519_uc010dlm.1_Intron	NM_145287	NP_660330			zinc finger protein 519						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	14184631	14184631	+	3'UTR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14184631delT	uc010xag.1	+	3					uc002ksv.1_Intron					RecName: Full=Putative ankyrin repeat domain-containing protein 20A5;																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	14681313	14681313	+	IGR	DEL	G	-	-	rs74521220		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14681313delG								POTEC (137714 upstream) : ANKRD30B (66926 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	15175254	15175254	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15175254delG								ANKRD30B (322517 upstream) : LOC644669 (138301 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	15384999	15384999	+	IGR	DEL	G	-	-	rs112267991		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15384999delG								LOC644669 (59081 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	15385208	15385209	+	IGR	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15385208_15385209delCT								LOC644669 (59290 upstream) : None (None downstream)																																			---	---	---	---
ROCK1	6093	broad.mit.edu	37	18	18588246	18588246	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:18588246delA	uc002kte.2	-							NM_005406	NP_005397			Rho-associated, coiled-coil containing protein						actin cytoskeleton organization|axon guidance|cellular component disassembly involved in apoptosis|cytokinesis|leukocyte tethering or rolling|membrane to membrane docking|Rho protein signal transduction	centriole|cytosol|Golgi membrane	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity			lung(2)|breast(2)|central_nervous_system(1)	5	Melanoma(1;0.165)																	---	---	---	---
GREB1L	80000	broad.mit.edu	37	18	18868697	18868698	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:18868697_18868698delTT	uc010xam.1	+						GREB1L_uc002ktf.1_Intron|GREB1L_uc010dlp.1_Intron	NM_001142966	NP_001136438			growth regulation by estrogen in breast							integral to membrane					0																		---	---	---	---
ESCO1	114799	broad.mit.edu	37	18	19144359	19144359	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19144359delT	uc002kth.1	-						ESCO1_uc002kti.1_Intron	NM_052911	NP_443143			establishment of cohesion 1 homolog 1						cell cycle|post-translational protein acetylation|regulation of DNA replication	chromatin|nucleus	acyltransferase activity|metal ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	19215241	19215241	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19215241delT								SNRPD1 (5033 upstream) : ABHD3 (15617 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	19549986	19549987	+	IGR	DEL	CT	-	-	rs76998390	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19549986_19549987delCT								MIB1 (99076 upstream) : GATA6 (199429 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	21069782	21069782	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21069782delA								RIOK3 (6685 upstream) : C18orf8 (13680 downstream)																																			---	---	---	---
TTC39C	125488	broad.mit.edu	37	18	21607241	21607242	+	Intron	DEL	AA	-	-	rs77633479		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21607241_21607242delAA	uc002kuw.2	+						TTC39C_uc002kuu.2_Intron	NM_001135993	NP_001129465			tetratricopeptide repeat domain 39C isoform 1								binding			ovary(1)	1																		---	---	---	---
ZNF521	25925	broad.mit.edu	37	18	22654116	22654116	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22654116delA	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	23307584	23307584	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23307584delC								ZNF521 (375370 upstream) : SS18 (288635 downstream)																																			---	---	---	---
TAF4B	6875	broad.mit.edu	37	18	23873535	23873535	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23873535delT	uc002kvu.3	+						TAF4B_uc002kvs.3_Intron|TAF4B_uc002kvt.3_Intron	NM_005640	NP_005631			TAF4b RNA polymerase II, TATA box binding						transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|nucleolus|transcription factor TFIID complex	DNA binding|NF-kappaB binding|sequence-specific DNA binding transcription factor activity			lung(1)|central_nervous_system(1)|skin(1)	3	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)															---	---	---	---
Unknown	0	broad.mit.edu	37	18	25081599	25081599	+	Intron	DEL	C	-	-	rs66545134		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25081599delC	uc002kwf.1	-											Homo sapiens cDNA FLJ45994 fis, clone SKMUS2009557.																														---	---	---	---
CDH2	1000	broad.mit.edu	37	18	25593923	25593923	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25593923delA	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	25971580	25971580	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25971580delA								CDH2 (214135 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	26425047	26425047	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:26425047delG								CDH2 (667602 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	27169189	27169190	+	IGR	INS	-	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:27169189_27169190insC								None (None upstream) : MIR302F (709686 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	28224787	28224788	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28224787_28224788insT								MIR302F (345861 upstream) : DSC3 (345265 downstream)																																			---	---	---	---
DSC2	1824	broad.mit.edu	37	18	28654582	28654583	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28654582_28654583delAA	uc002kwl.3	-						DSC2_uc002kwk.3_Intron	NM_024422	NP_077740			desmocollin 2 isoform Dsc2a preproprotein						homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			ovary(2)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(10;0.0241)															---	---	---	---
DSC1	1823	broad.mit.edu	37	18	28730458	28730460	+	Intron	DEL	CAC	-	-	rs141461651		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28730458_28730460delCAC	uc002kwn.2	-						DSC1_uc002kwm.2_Intron	NM_024421	NP_077739			desmocollin 1 isoform Dsc1a preproprotein						homophilic cell adhesion	desmosome|gap junction|integral to membrane|membrane fraction	calcium ion binding			ovary(3)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(10;0.00778)															---	---	---	---
Unknown	0	broad.mit.edu	37	18	28848177	28848177	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28848177delT								DSC1 (105358 upstream) : DSG1 (49875 downstream)																																			---	---	---	---
DSG2	1829	broad.mit.edu	37	18	29115731	29115731	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29115731delA	uc002kwu.3	+							NM_001943	NP_001934			desmoglein 2 preproprotein						cellular component disassembly involved in apoptosis|homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			central_nervous_system(5)|ovary(2)|breast(1)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(10;0.0068)															---	---	---	---
Unknown	0	broad.mit.edu	37	18	29313057	29313057	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29313057delA								B4GALT6 (48371 upstream) : MCART2 (26602 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	29576349	29576349	+	IGR	DEL	A	-	-	rs71936173		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29576349delA								KIAA1012 (53250 upstream) : RNF125 (22096 downstream)																																			---	---	---	---
RNF125	54941	broad.mit.edu	37	18	29597505	29597505	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29597505delT	uc002kxf.1	+							NM_017831	NP_060301			ring finger protein 125						negative regulation of type I interferon production	intracellular	ligase activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	29713526	29713527	+	IGR	INS	-	T	T	rs34753197		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29713526_29713527insT								RNF138 (2003 upstream) : MEP1B (56460 downstream)																																			---	---	---	---
MEP1B	4225	broad.mit.edu	37	18	29774790	29774790	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29774790delT	uc002kxj.3	+							NM_005925	NP_005916			meprin A beta precursor						digestion|proteolysis	extracellular space|integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
FAM59A	64762	broad.mit.edu	37	18	29921979	29921979	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29921979delA	uc002kxl.2	-						FAM59A_uc002kxk.1_Intron	NM_022751	NP_073588			family with sequence similarity 59, member A											ovary(1)|skin(1)	2																		---	---	---	---
KLHL14	57565	broad.mit.edu	37	18	30349570	30349570	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30349570delC	uc002kxm.1	-							NM_020805	NP_065856			kelch-like 14							cytosol|endoplasmic reticulum membrane				ovary(1)	1																		---	---	---	---
ASXL3	80816	broad.mit.edu	37	18	31194786	31194786	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31194786delT	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																		---	---	---	---
NOL4	8715	broad.mit.edu	37	18	31614807	31614807	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31614807delA	uc010dmi.2	-						NOL4_uc010xbs.1_Intron|NOL4_uc002kxr.3_Intron|NOL4_uc010xbt.1_Intron|NOL4_uc010dmh.2_Intron|NOL4_uc010xbu.1_Intron|NOL4_uc002kxt.3_Intron|NOL4_uc010xbw.1_Intron	NM_003787	NP_003778			nucleolar protein 4							nucleolus	RNA binding			ovary(3)	3																		---	---	---	---
NOL4	8715	broad.mit.edu	37	18	31675216	31675219	+	Intron	DEL	TGTG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31675216_31675219delTGTG	uc010dmi.2	-						NOL4_uc002kxr.3_Intron|NOL4_uc010xbt.1_Intron|NOL4_uc010dmh.2_Intron|NOL4_uc010xbu.1_Intron|NOL4_uc002kxt.3_Intron|NOL4_uc010xbw.1_Intron	NM_003787	NP_003778			nucleolar protein 4							nucleolus	RNA binding			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	31923278	31923278	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31923278delT								NOL4 (119832 upstream) : DTNA (149976 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	32001576	32001578	+	IGR	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32001576_32001578delTTT								NOL4 (198130 upstream) : DTNA (71676 downstream)																																			---	---	---	---
DTNA	1837	broad.mit.edu	37	18	32182663	32182663	+	Intron	DEL	A	-	-	rs78090135		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32182663delA	uc010dmj.2	+						DTNA_uc002kxu.2_Intron|DTNA_uc010xbx.1_Intron|DTNA_uc002kxv.3_Intron|DTNA_uc002kxw.2_Intron|DTNA_uc002kxx.2_Intron|DTNA_uc002kxz.2_Intron|DTNA_uc002kxy.2_Intron	NM_032975	NP_116757			dystrobrevin alpha isoform 2						neuromuscular synaptic transmission|signal transduction|striated muscle contraction	cell junction|cytoplasm|synapse	calcium ion binding|protein binding|zinc ion binding				0																		---	---	---	---
DTNA	1837	broad.mit.edu	37	18	32377973	32377973	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32377973delT	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	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																		---	---	---	---
MAPRE2	10982	broad.mit.edu	37	18	32576019	32576019	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32576019delT	uc010xcc.1	+						MAPRE2_uc010xcb.1_Intron	NM_001143827	NP_001137299			microtubule-associated protein, RP/EB family,						cell division|cell proliferation|mitosis|signal transduction	cytoplasm|microtubule	microtubule binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	32992658	32992658	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32992658delT								ZNF396 (35357 upstream) : INO80C (40632 downstream)																																			---	---	---	---
SLC39A6	25800	broad.mit.edu	37	18	33704734	33704734	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33704734delT	uc010dmy.2	-						SLC39A6_uc002kzj.2_Intron	NM_012319	NP_036451			solute carrier family 39 (zinc transporter),							integral to membrane|lamellipodium membrane	zinc ion transmembrane transporter activity			ovary(1)|pancreas(1)	2																		---	---	---	---
MOCOS	55034	broad.mit.edu	37	18	33822983	33822983	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33822983delT	uc002kzq.3	+							NM_017947	NP_060417			molybdenum cofactor sulfurase						Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cytosol	lyase activity|Mo-molybdopterin cofactor sulfurase activity|molybdenum ion binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)													---	---	---	---
CELF4	56853	broad.mit.edu	37	18	35146711	35146711	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35146711delT	uc002lae.2	-						CELF4_uc010dnd.1_5'Flank|CELF4_uc002lag.2_5'Flank|CELF4_uc002laf.2_5'Flank|CELF4_uc002lai.2_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																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	35614984	35614984	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35614984delA								CELF4 (468984 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	35649261	35649261	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35649261delT								CELF4 (503261 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	36029273	36029274	+	IGR	DEL	CA	-	-	rs10561068		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:36029273_36029274delCA								CELF4 (883273 upstream) : LOC647946 (757614 downstream)																																			---	---	---	---
LOC647946	647946	broad.mit.edu	37	18	37058132	37058132	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37058132delT	uc010xcj.1	-						LOC647946_uc002lal.1_Intron	NR_024391				Homo sapiens cDNA FLJ33284 fis, clone ASTRO2009458.												0																		---	---	---	---
LOC647946	647946	broad.mit.edu	37	18	37154375	37154375	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37154375delA	uc010xcj.1	-						LOC647946_uc002lal.1_Intron	NR_024391				Homo sapiens cDNA FLJ33284 fis, clone ASTRO2009458.												0																		---	---	---	---
LOC647946	647946	broad.mit.edu	37	18	37200259	37200259	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37200259delA	uc010xcj.1	-						LOC647946_uc002lal.1_Intron	NR_024391				Homo sapiens cDNA FLJ33284 fis, clone ASTRO2009458.												0																		---	---	---	---
LOC647946	647946	broad.mit.edu	37	18	37222124	37222126	+	Intron	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37222124_37222126delAAA	uc010xcj.1	-						LOC647946_uc002lal.1_Intron	NR_024391				Homo sapiens cDNA FLJ33284 fis, clone ASTRO2009458.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	38009851	38009851	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38009851delA								LOC647946 (629569 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	38159976	38159978	+	IGR	DEL	AAA	-	-	rs77234440		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38159976_38159978delAAA								LOC647946 (779694 upstream) : KC6 (900260 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	38899228	38899228	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38899228delA								None (None upstream) : KC6 (161010 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	39860572	39860573	+	Intron	INS	-	AT	AT			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39860572_39860573insAT	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	40004473	40004473	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40004473delT	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	40307922	40307922	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40307922delT								PIK3C3 (646478 upstream) : RIT2 (15271 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	41537103	41537103	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41537103delA								SYT4 (679488 upstream) : SETBP1 (723035 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	41631215	41631215	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41631215delA								SYT4 (773600 upstream) : SETBP1 (628923 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	41929018	41929018	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41929018delT	uc002lax.3	-											Homo sapiens cDNA clone IMAGE:5265929.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	42204937	42204938	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42204937_42204938insT								None (None upstream) : SETBP1 (55200 downstream)																																			---	---	---	---
SETBP1	26040	broad.mit.edu	37	18	42621942	42621942	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42621942delA	uc010dni.2	+							NM_015559	NP_056374			SET binding protein 1 isoform a							nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)										Schinzel-Giedion_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	18	42705815	42705815	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42705815delA								SETBP1 (57342 upstream) : SLC14A2 (42158 downstream)																																			---	---	---	---
SLC14A2	8170	broad.mit.edu	37	18	42863923	42863923	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42863923delA	uc010dnj.2	+						SLC14A2_uc002lbb.2_Intron	NM_007163	NP_009094			solute carrier family 14 (urea transporter),							apical plasma membrane|integral to membrane|membrane fraction	protein binding|urea transmembrane transporter activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	43425306	43425306	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43425306delC								SIGLEC15 (2785 upstream) : KIAA1632 (2269 downstream)																																			---	---	---	---
KIAA1632	57724	broad.mit.edu	37	18	43529365	43529365	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	43662665	43662665	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43662665delA								PSTPIP2 (10415 upstream) : ATP5A1 (1445 downstream)																																			---	---	---	---
C18orf25	147339	broad.mit.edu	37	18	43845881	43845882	+	3'UTR	DEL	TT	-	-	rs147292147		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43845881_43845882delTT	uc002lbw.2	+	6					C18orf25_uc002lbx.2_3'UTR	NM_145055	NP_659492			ARKadia-like 1 isoform a											central_nervous_system(2)	2																		---	---	---	---
KATNAL2	83473	broad.mit.edu	37	18	44520645	44520645	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44520645delG	uc010dnq.1	+											SubName: Full=Putative uncharacterized protein DKFZp667C165; Flags: Fragment;							cytoplasm|microtubule	ATP binding|microtubule-severing ATPase activity			ovary(1)|skin(1)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
IER3IP1	51124	broad.mit.edu	37	18	44682386	44682388	+	3'UTR	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44682386_44682388delAAA	uc002lcu.2	-	3						NM_016097	NP_057181			immediate early response 3 interacting protein							endoplasmic reticulum membrane|Golgi apparatus|integral to membrane					0																		---	---	---	---
IER3IP1	51124	broad.mit.edu	37	18	44682614	44682614	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44682614delA	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	44858344	44858345	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44858344_44858345delAA	uc002lcx.2	+											Homo sapiens, clone IMAGE:5538207, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	45285750	45285751	+	IGR	INS	-	A	A	rs34750051		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45285750_45285751insA								IER3IP1 (583005 upstream) : SMAD2 (73716 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	47202345	47202346	+	IGR	DEL	AA	-	-	rs35295951		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47202345_47202346delAA								LIPG (83069 upstream) : ACAA2 (107529 downstream)																																			---	---	---	---
MYO5B	4645	broad.mit.edu	37	18	47699648	47699649	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47699648_47699649delAA	uc002leb.2	-							NM_001080467	NP_001073936			myosin VB						protein transport	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(2)|central_nervous_system(1)	5				READ - Rectum adenocarcinoma(32;0.103)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	47836226	47836227	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47836226_47836227delTC								CXXC1 (21534 upstream) : SKA1 (65165 downstream)																																			---	---	---	---
MAPK4	5596	broad.mit.edu	37	18	48230852	48230852	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48230852delA	uc002lev.2	+						MAPK4_uc010xdm.1_Intron|MAPK4_uc010doz.2_Intron	NM_002747	NP_002738			mitogen-activated protein kinase 4						cell cycle		ATP binding|MAP kinase activity			lung(4)|skin(2)	6		Colorectal(6;0.0297)		Colorectal(21;0.156)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	48770153	48770154	+	IGR	INS	-	TG	TG	rs144994612	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48770153_48770154insTG								MEX3C (46463 upstream) : None (None downstream)																																			---	---	---	---
MBD2	8932	broad.mit.edu	37	18	51710062	51710063	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51710062_51710063delAC	uc002lfg.1	-							NM_003927	NP_003918			methyl-CpG binding domain protein 2 isoform 1						transcription, DNA-dependent		C2H2 zinc finger domain binding|methyl-CpG binding|satellite DNA binding				0				Colorectal(16;0.0212)|READ - Rectum adenocarcinoma(32;0.188)	Hexobarbital(DB01355)													---	---	---	---
TCF4	6925	broad.mit.edu	37	18	53021363	53021363	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53021363delT	uc002lfz.2	-						TCF4_uc010xdu.1_Intron|TCF4_uc010xdv.1_Intron|TCF4_uc002lfx.2_Intron|TCF4_uc010xdw.1_Intron|TCF4_uc002lfy.2_Intron|TCF4_uc010xdx.1_Intron|TCF4_uc010dph.1_Intron|TCF4_uc010xdy.1_Intron|TCF4_uc002lga.2_Intron|TCF4_uc010dpi.2_Intron|TCF4_uc002lgc.3_Intron	NM_003199	NP_003190			transcription factor 4 isoform b						positive regulation of neuron differentiation|protein-DNA complex assembly|transcription initiation from RNA polymerase II promoter	transcription factor complex	E-box binding|protein C-terminus binding|protein heterodimerization activity|RNA polymerase II core promoter proximal region sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity|TFIIB-class binding transcription factor activity|TFIIB-class transcription factor binding			ovary(1)|lung(1)	2				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	53660534	53660534	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53660534delT								TCF4 (357349 upstream) : TXNL1 (609521 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	54146906	54146906	+	IGR	DEL	T	-	-	rs75878324		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54146906delT								TCF4 (843721 upstream) : TXNL1 (123149 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	54250362	54250362	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54250362delA								TCF4 (947177 upstream) : TXNL1 (19693 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	55196090	55196090	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55196090delA								ONECUT2 (37561 upstream) : FECH (15984 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	55525792	55525792	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55525792delA								ATP8B1 (126753 upstream) : NEDD4L (185827 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	55531369	55531371	+	IGR	DEL	ATC	-	-	rs67724569		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55531369_55531371delATC								ATP8B1 (132330 upstream) : NEDD4L (180248 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	55625987	55625987	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55625987delA								ATP8B1 (226948 upstream) : NEDD4L (85632 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	55658339	55658339	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55658339delA								ATP8B1 (259300 upstream) : NEDD4L (53280 downstream)																																			---	---	---	---
NEDD4L	23327	broad.mit.edu	37	18	55901482	55901482	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55901482delT	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																		---	---	---	---
SEC11C	90701	broad.mit.edu	37	18	56816528	56816528	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56816528delT	uc002lht.2	+						SEC11C_uc010dpo.1_Intron|SEC11C_uc010xej.1_Intron	NM_033280	NP_150596			SEC11-like 3						energy reserve metabolic process|regulation of insulin secretion|signal peptide processing	endoplasmic reticulum membrane|integral to membrane|microsome	serine-type peptidase activity				0		Colorectal(73;0.175)																---	---	---	---
LMAN1	3998	broad.mit.edu	37	18	57013194	57013194	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57013194delT	uc002lhz.2	-	8	944	c.912delA	c.(910-912)AAAfs	p.K304fs		NM_005570	NP_005561	P49257	LMAN1_HUMAN	lectin, mannose-binding, 1 precursor	304	Lumenal (Potential).				blood coagulation|ER to Golgi vesicle-mediated transport|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|protein transport	endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane	mannose binding|metal ion binding|unfolded protein binding			skin(1)	1		Colorectal(73;0.0946)			Antihemophilic Factor(DB00025)													---	---	---	---
CCBE1	147372	broad.mit.edu	37	18	57125354	57125357	+	Intron	DEL	ATCC	-	-	rs111727745		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57125354_57125357delATCC	uc002lib.2	-						CCBE1_uc002lia.2_5'Flank	NM_133459	NP_597716			collagen and calcium binding EGF domains 1						lymphangiogenesis|sprouting angiogenesis|venous blood vessel morphogenesis	collagen	calcium ion binding			skin(2)|ovary(1)	3		Colorectal(73;0.175)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	57454546	57454546	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57454546delA								CCBE1 (89902 upstream) : PMAIP1 (112646 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	57523906	57523907	+	IGR	DEL	AC	-	-	rs34424123		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57523906_57523907delAC								CCBE1 (159262 upstream) : PMAIP1 (43285 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	57593262	57593262	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57593262delT								PMAIP1 (21724 upstream) : MC4R (445302 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	58598787	58598787	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58598787delT								MC4R (558786 upstream) : CDH20 (402201 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	58790045	58790047	+	IGR	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58790045_58790047delTTT								MC4R (750044 upstream) : CDH20 (210941 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	58838377	58838379	+	IGR	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58838377_58838379delAAA								MC4R (798376 upstream) : CDH20 (162609 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	59399213	59399213	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59399213delA								CDH20 (176848 upstream) : RNF152 (83091 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	59703499	59703499	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59703499delT								RNF152 (143195 upstream) : PIGN (7961 downstream)																																			---	---	---	---
KIAA1468	57614	broad.mit.edu	37	18	59888803	59888803	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59888803delT	uc002lil.2	+						KIAA1468_uc002lik.1_Intron|KIAA1468_uc010xel.1_Intron|KIAA1468_uc002lim.2_Intron	NM_020854	NP_065905			hypothetical protein LOC57614								binding			ovary(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)	6		Colorectal(73;0.186)																---	---	---	---
ZCCHC2	54877	broad.mit.edu	37	18	60234500	60234501	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60234500_60234501insT	uc002lip.3	+						ZCCHC2_uc002lio.2_Intron|ZCCHC2_uc002liq.2_Intron	NM_017742	NP_060212			zinc finger, CCHC domain containing 2						cell communication	cytoplasm	nucleic acid binding|phosphatidylinositol binding|zinc ion binding			lung(1)|prostate(1)	2																		---	---	---	---
PHLPP1	23239	broad.mit.edu	37	18	60446491	60446491	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60446491delT	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																		---	---	---	---
SERPINB11	89778	broad.mit.edu	37	18	61367308	61367310	+	5'Flank	DEL	TCC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61367308_61367310delTCC	uc002ljk.3	+						SERPINB11_uc010xes.1_5'Flank|SERPINB11_uc010dqd.2_5'Flank	NM_080475	NP_536723			serpin peptidase inhibitor, clade B, member 11						regulation of proteolysis	cytoplasm	serine-type endopeptidase inhibitor activity			breast(1)	1		Esophageal squamous(42;0.129)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	61503587	61503588	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61503587_61503588delTT								SERPINB7 (30984 upstream) : SERPINB2 (51351 downstream)																																			---	---	---	---
SERPINB2	5055	broad.mit.edu	37	18	61553533	61553533	+	5'Flank	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61553533delA	uc010xeu.1	+						SERPINB2_uc002ljo.2_5'Flank|SERPINB2_uc010dqh.2_5'Flank	NM_001143818	NP_001137290			serine (or cysteine) proteinase inhibitor, clade						anti-apoptosis|blood coagulation|fibrinolysis|regulation of proteolysis	extracellular space|Golgi apparatus|plasma membrane	serine-type endopeptidase inhibitor activity			lung(1)|skin(1)	2		Esophageal squamous(42;0.131)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)|Urokinase(DB00013)													---	---	---	---
Unknown	0	broad.mit.edu	37	18	62604726	62604727	+	IGR	DEL	CA	-	-	rs35570118		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62604726_62604727delCA								C18orf20 (788466 upstream) : CDH7 (812761 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	63076464	63076465	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63076464_63076465delTC								None (None upstream) : CDH7 (341023 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	63870788	63870788	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63870788delA								CDH7 (322614 upstream) : CDH19 (300533 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	64076241	64076241	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64076241delT								CDH7 (528067 upstream) : CDH19 (95080 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	64166723	64166724	+	IGR	INS	-	TTAA	TTAA	rs149629367	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64166723_64166724insTTAA								CDH7 (618549 upstream) : CDH19 (4597 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	64764936	64764937	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64764936_64764937delAA								CDH19 (493720 upstream) : DSEL (408882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	66745530	66745530	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66745530delA								CCDC102B (23104 upstream) : DOK6 (322761 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	68079733	68079733	+	IGR	DEL	T	-	-	rs111425830		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68079733delT								SOCS6 (82299 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	69730170	69730171	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:69730170_69730171delTT								None (None upstream) : CBLN2 (473744 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	70222683	70222684	+	IGR	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:70222683_70222684delGT								CBLN2 (10960 upstream) : NETO1 (186867 downstream)																																			---	---	---	---
NETO1	81832	broad.mit.edu	37	18	70423237	70423238	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:70423237_70423238insT	uc002lkw.2	-						NETO1_uc002lkx.1_Intron|NETO1_uc002lky.1_Intron	NM_138966	NP_620416			neuropilin- and tolloid-like protein 1 isoform 3						memory|regulation of long-term neuronal synaptic plasticity|visual learning	cell junction|excitatory synapse|extracellular region|integral to membrane|postsynaptic density|postsynaptic membrane	receptor activity			ovary(2)|skin(2)	4		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	70840075	70840075	+	RNA	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:70840075delG	uc002lla.1	-	4		c.607delC			uc002llb.2_Intron					Homo sapiens cDNA clone IMAGE:3842655.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	71674927	71674928	+	IGR	INS	-	CT	CT	rs149777060	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71674927_71674928insCT								None (None upstream) : FBXO15 (65660 downstream)																																			---	---	---	---
ZNF407	55628	broad.mit.edu	37	18	72391995	72391995	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72391995delT	uc002llw.2	+						ZNF407_uc010xfc.1_Intron|ZNF407_uc010dqu.1_Intron	NM_017757	NP_060227			zinc finger protein 407 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)														---	---	---	---
ZNF407	55628	broad.mit.edu	37	18	72673876	72673876	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72673876delT	uc002llw.2	+							NM_017757	NP_060227			zinc finger protein 407 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	72819292	72819292	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72819292delA								ZNF407 (41664 upstream) : ZADH2 (89987 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	73070283	73070283	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73070283delT								TSHZ1 (68383 upstream) : C18orf62 (51544 downstream)																																			---	---	---	---
C18orf62	284274	broad.mit.edu	37	18	73135994	73135997	+	Intron	DEL	TGTT	-	-	rs77402983		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73135994_73135997delTGTT	uc002lma.1	-						C18orf62_uc010dqw.1_Intron|C18orf62_uc002lmb.1_Intron	NM_001037331	NP_001032408			hypothetical protein LOC284274							integral to membrane					0		Esophageal squamous(42;0.131)|Prostate(75;0.155)		OV - Ovarian serous cystadenocarcinoma(15;6.21e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	73585509	73585512	+	IGR	DEL	ACAC	-	-	rs34117404		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73585509_73585512delACAC								C18orf62 (445920 upstream) : ZNF516 (486107 downstream)																																			---	---	---	---
LOC284276	284276	broad.mit.edu	37	18	74246835	74246836	+	Intron	INS	-	TGA	TGA			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74246835_74246836insTGA	uc002lmg.2	+							NR_015417				Homo sapiens cDNA FLJ36617 fis, clone TRACH2016481.												0																		---	---	---	---
MBP	4155	broad.mit.edu	37	18	74797983	74797984	+	Intron	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74797983_74797984delAG	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	75367843	75367843	+	IGR	DEL	G	-	-	rs11285447		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75367843delG								GALR1 (385749 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	76722078	76722083	+	IGR	DEL	ACTCTC	-	-	rs72439716		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76722078_76722083delACTCTC								None (None upstream) : SALL3 (18192 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	77410832	77410832	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77410832delG								NFATC1 (121510 upstream) : CTDP1 (28969 downstream)																																			---	---	---	---
PPAP2C	8612	broad.mit.edu	37	19	285599	285600	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:285599_285600delAA	uc002loi.2	-						PPAP2C_uc002loh.2_Intron|PPAP2C_uc002loj.2_Intron	NM_003712	NP_003703			phosphatidic acid phosphatase type 2C isoform 1						sphingolipid metabolic process	integral to membrane|plasma membrane	phosphatidate phosphatase activity|phosphoprotein phosphatase activity|sphingosine-1-phosphate phosphatase activity			central_nervous_system(1)	1		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	351309	351310	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:351309_351310delAC								MIER2 (6518 upstream) : THEG (10749 downstream)																																			---	---	---	---
ABCA7	10347	broad.mit.edu	37	19	1046580	1046581	+	Intron	DEL	GG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1046580_1046581delGG	uc002lqw.3	+						ABCA7_uc010dsb.1_Intron	NM_019112	NP_061985			ATP-binding cassette, sub-family A, member 7						phagocytosis|transmembrane transport	ATP-binding cassette (ABC) transporter complex|endosome membrane|Golgi membrane|integral to membrane|plasma membrane	ATP binding|ATPase activity|transporter activity			pancreas(7)|ovary(1)|central_nervous_system(1)	9		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
ADAMTSL5	339366	broad.mit.edu	37	19	1509069	1509069	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1509069delC	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	1670115	1670115	+	IGR	DEL	C	-	-	rs147408750		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1670115delC								TCF3 (17789 upstream) : ONECUT3 (83547 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	1680307	1680310	+	IGR	DEL	TTTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1680307_1680310delTTTT								TCF3 (27981 upstream) : ONECUT3 (73352 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	1899992	1899992	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1899992delC								FAM108A1 (14474 upstream) : SCAMP4 (5381 downstream)																																			---	---	---	---
LMNB2	84823	broad.mit.edu	37	19	2451834	2451835	+	Intron	INS	-	G	G	rs138241094	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2451834_2451835insG	uc002lvy.2	-						LMNB2_uc002lwa.1_Intron	NM_032737	NP_116126			lamin B2							nuclear inner membrane	structural molecule activity			large_intestine(1)|ovary(1)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	2857840	2857840	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2857840delA								ZNF555 (3634 upstream) : ZNF556 (9493 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	3083933	3083934	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3083933_3083934delTT								AES (20969 upstream) : GNA11 (10474 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	3089552	3089552	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3089552delA								AES (26588 upstream) : GNA11 (4856 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	3316167	3316167	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3316167delA								CELF5 (19096 upstream) : NFIC (43449 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	3332891	3332891	+	IGR	DEL	T	-	-	rs142857348	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3332891delT								CELF5 (35820 upstream) : NFIC (26725 downstream)																																			---	---	---	---
NFIC	4782	broad.mit.edu	37	19	3400477	3400477	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3400477delA	uc010xhi.1	+						NFIC_uc002lxo.2_Intron|NFIC_uc010xhh.1_Intron|NFIC_uc002lxp.2_Intron|NFIC_uc010xhj.1_Intron|NFIC_uc002lxq.1_Intron	NM_205843	NP_995315			nuclear factor I/C isoform 2						DNA replication|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|sequence-specific DNA binding transcription factor activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.8e-05)|Epithelial(107;2.94e-108)|BRCA - Breast invasive adenocarcinoma(158;0.00154)|STAD - Stomach adenocarcinoma(1328;0.191)														---	---	---	---
ZFR2	23217	broad.mit.edu	37	19	3871980	3871980	+	5'Flank	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3871980delA	uc002lyw.2	-						ZFR2_uc010xhx.1_5'Flank|ZFR2_uc002lyx.3_5'Flank|ZFR2_uc010xhy.1_5'Flank	NM_015174	NP_055989			zinc finger RNA binding protein 2 isoform 1							intracellular	nucleic acid binding|zinc ion binding			central_nervous_system(1)|pancreas(1)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00514)|STAD - Stomach adenocarcinoma(1328;0.19)														---	---	---	---
DPP9	91039	broad.mit.edu	37	19	4714327	4714327	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4714327delC	uc002mba.2	-	4	337	c.79delG	c.(79-81)GCTfs	p.A27fs	DPP9_uc002mbb.2_Frame_Shift_Del_p.A27fs|DPP9_uc002mbc.2_Frame_Shift_Del_p.A27fs	NM_139159	NP_631898	Q86TI2	DPP9_HUMAN	dipeptidylpeptidase 9	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					proteolysis	cytosol|membrane	aminopeptidase activity|serine-type peptidase activity			skin(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00884)														---	---	---	---
PLIN3	10226	broad.mit.edu	37	19	4861949	4861950	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4861949_4861950insT	uc002mbj.2	-						PLIN3_uc002mbk.2_Intron|PLIN3_uc002mbl.3_Intron	NM_005817	NP_005808			mannose 6 phosphate receptor binding protein 1						vesicle-mediated transport	endosome membrane|Golgi apparatus|lipid particle	protein binding				0					Galsulfase(DB01279)|Idursulfase(DB01271)													---	---	---	---
KDM4B	23030	broad.mit.edu	37	19	4989341	4989341	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4989341delT	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																		---	---	---	---
TMEM146	257062	broad.mit.edu	37	19	5735489	5735490	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5735489_5735490delTT	uc002mda.2	+						TMEM146_uc010duj.1_Intron	NM_152784	NP_689997			transmembrane protein 146 precursor							integral to membrane				ovary(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
TMEM146	257062	broad.mit.edu	37	19	5753884	5753884	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5753884delA	uc002mda.2	+						TMEM146_uc010duj.1_Intron	NM_152784	NP_689997			transmembrane protein 146 precursor							integral to membrane				ovary(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
KHSRP	8570	broad.mit.edu	37	19	6414223	6414223	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6414223delG	uc002mer.3	-							NM_003685	NP_003676			KH-type splicing regulatory protein						mRNA processing|mRNA transport|regulation of transcription, DNA-dependent|RNA splicing, via transesterification reactions|transcription, DNA-dependent	cytosol|nucleus	DNA binding|protein binding|RNA binding			skin(1)	1																		---	---	---	---
CRB3	92359	broad.mit.edu	37	19	6466212	6466212	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6466212delA	uc002mey.2	+						CRB3_uc002mez.2_Intron|CRB3_uc002mfa.2_Intron	NM_139161	NP_631900			crumbs 3 isoform a precursor						protein localization in plasma membrane|tight junction assembly	apical plasma membrane|integral to membrane|tight junction	SH3 domain binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	6562770	6562770	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6562770delT								TNFSF9 (26831 upstream) : CD70 (20365 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	6581061	6581068	+	IGR	DEL	CTTCCCTC	-	-	rs116048035	by1000genomes;by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6581061_6581068delCTTCCCTC								TNFSF9 (45122 upstream) : CD70 (2067 downstream)																																			---	---	---	---
SH2D3A	10045	broad.mit.edu	37	19	6760567	6760567	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6760567delA	uc002mft.2	-						SH2D3A_uc010xjg.1_Intron	NM_005490	NP_005481			SH2 domain containing 3A						JNK cascade|small GTPase mediated signal transduction	intracellular	guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			breast(2)	2																		---	---	---	---
EMR1	2015	broad.mit.edu	37	19	6918451	6918452	+	Intron	INS	-	AA	AA			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6918451_6918452insAA	uc002mfw.2	+						EMR1_uc010dvc.2_Intron|EMR1_uc010dvb.2_Intron|EMR1_uc010xji.1_Intron|EMR1_uc010xjj.1_Intron	NM_001974	NP_001965			egf-like module containing, mucin-like, hormone						cell adhesion|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(3)|lung(1)|skin(1)	5	all_hematologic(4;0.166)																	---	---	---	---
INSR	3643	broad.mit.edu	37	19	7214908	7214908	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7214908delT	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)													---	---	---	---
INSR	3643	broad.mit.edu	37	19	7270328	7270329	+	Intron	DEL	TC	-	-	rs138733954	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7270328_7270329delTC	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	7452723	7452723	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7452723delT	uc010xjm.1	+							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)																---	---	---	---
ZNF358	140467	broad.mit.edu	37	19	7583433	7583434	+	Intron	INS	-	AA	AA	rs145336819	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7583433_7583434insAA	uc002mgn.2	+							NM_018083	NP_060553			zinc finger protein 358						embryonic forelimb morphogenesis|neural tube development|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
XAB2	56949	broad.mit.edu	37	19	7691237	7691237	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7691237delC	uc002mgx.2	-							NM_020196	NP_064581			XPA binding protein 2						transcription, DNA-dependent|transcription-coupled nucleotide-excision repair	catalytic step 2 spliceosome|nucleoplasm	protein binding			central_nervous_system(2)|breast(1)|skin(1)	4													Direct_reversal_of_damage|NER					---	---	---	---
FCER2	2208	broad.mit.edu	37	19	7767509	7767509	+	5'Flank	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7767509delA	uc002mhn.2	-						FCER2_uc010xjs.1_5'Flank|FCER2_uc010xjt.1_5'Flank|FCER2_uc002mhm.2_5'Flank|FCER2_uc010dvo.2_5'Flank	NM_002002	NP_001993			Fc fragment of IgE, low affinity II, receptor						positive regulation of killing of cells of other organism|positive regulation of nitric-oxide synthase 2 biosynthetic process|positive regulation of nitric-oxide synthase activity	extracellular region|integral to plasma membrane	IgE binding|integrin binding|receptor activity|sugar binding				0																		---	---	---	---
KANK3	256949	broad.mit.edu	37	19	8392519	8392519	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8392519delA	uc010dwa.2	-							NM_198471	NP_940873			ankyrin repeat domain 47												0																		---	---	---	---
ADAMTS10	81794	broad.mit.edu	37	19	8664728	8664728	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8664728delT	uc002mkj.1	-						ADAMTS10_uc002mkk.1_Intron	NM_030957	NP_112219			ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			pancreas(2)|skin(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	8773556	8773557	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8773556_8773557delTG								ADAMTS10 (97968 upstream) : ACTL9 (34194 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	8900995	8900998	+	IGR	DEL	GAAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8900995_8900998delGAAA								OR2Z1 (58661 upstream) : ZNF558 (19384 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	9184450	9184451	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9184450_9184451delAA								MUC16 (92432 upstream) : OR1M1 (19470 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	9713365	9713366	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9713365_9713366delTT								ZNF121 (18156 upstream) : ZNF561 (4637 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	9909625	9909625	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9909625delA								ZNF846 (30215 upstream) : FBXL12 (11320 downstream)																																			---	---	---	---
RDH8	50700	broad.mit.edu	37	19	10128631	10128631	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10128631delT	uc002mmr.2	+							NM_015725	NP_056540			retinol dehydrogenase 8 (all-trans)						estrogen biosynthetic process|response to stimulus|visual perception	cytoplasm|integral to plasma membrane	binding|estradiol 17-beta-dehydrogenase activity|NADP-retinol dehydrogenase activity|retinol dehydrogenase activity			ovary(3)|pancreas(1)	4			Epithelial(33;4.24e-05)		Vitamin A(DB00162)													---	---	---	---
C3P1	388503	broad.mit.edu	37	19	10150891	10150892	+	5'Flank	INS	-	AA	AA	rs141908820		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10150891_10150892insAA	uc010dwx.1	+							NR_027300				Synthetic construct DNA, clone: pF1KB7402, Homo sapiens LOC388503 gene, without stop codon, in Flexi system.												0																		---	---	---	---
C3P1	388503	broad.mit.edu	37	19	10177055	10177056	+	Intron	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10177055_10177056delAG	uc010dwx.1	+							NR_027300				Synthetic construct DNA, clone: pF1KB7402, Homo sapiens LOC388503 gene, without stop codon, in Flexi system.												0																		---	---	---	---
DNMT1	1786	broad.mit.edu	37	19	10288073	10288073	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10288073delA	uc002mng.2	-						DNMT1_uc010xlc.1_Intron|DNMT1_uc002mnh.2_Intron|DNMT1_uc010xld.1_Intron|DNMT1_uc010dxb.1_Intron	NM_001379	NP_001370			DNA (cytosine-5-)-methyltransferase 1 isoform b						chromatin modification|maintenance of DNA methylation|negative regulation of histone H3-K9 methylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene expression|positive regulation of histone H3-K4 methylation|transcription, DNA-dependent	nucleus	DNA (cytosine-5-)-methyltransferase activity|DNA binding|transcription factor binding			ovary(2)|prostate(1)|lung(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Ifosfamide(DB01181)|Procainamide(DB01035)													---	---	---	---
MRPL4	51073	broad.mit.edu	37	19	10367123	10367123	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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	10427738	10427738	+	3'UTR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10427738delG	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)															---	---	---	---
SMARCA4	6597	broad.mit.edu	37	19	11162168	11162171	+	Intron	DEL	TTTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11162168_11162171delTTTT	uc002mqf.3	+						SMARCA4_uc010dxp.2_Intron|SMARCA4_uc010dxo.2_Intron|SMARCA4_uc010dxq.2_Intron|SMARCA4_uc010dxr.2_Intron|SMARCA4_uc002mqj.3_Intron|SMARCA4_uc010dxs.2_Intron|SMARCA4_uc002mqh.3_Intron	NM_003072	NP_003063			SWI/SNF-related matrix-associated						chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity			lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1)	67		all_lung(6;0.0512)|Lung NSC(9;0.0568)						F|N|Mis		NSCLC				Rhabdoid_Predisposition_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	19	11192318	11192318	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11192318delT								SMARCA4 (19359 upstream) : LDLR (7739 downstream)																																			---	---	---	---
DOCK6	57572	broad.mit.edu	37	19	11326767	11326768	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11326767_11326768delTT	uc002mqs.3	-						DOCK6_uc010xlq.1_Intron	NM_020812	NP_065863			dedicator of cytokinesis 6						blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(2)|skin(1)	3																		---	---	---	---
EPOR	2057	broad.mit.edu	37	19	11488473	11488473	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11488473delA	uc002mrh.2	-	2										SubName: Full=Erythropoietin receptor; Flags: Fragment;							extracellular region|integral to plasma membrane	erythropoietin receptor activity|identical protein binding			ovary(1)	1					Darbepoetin alfa(DB00012)|Epoetin alfa(DB00016)											OREG0025254	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ZNF833	401898	broad.mit.edu	37	19	11775607	11775609	+	Intron	DEL	AAT	-	-	rs5827133		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11775607_11775609delAAT	uc002msl.3	+											Homo sapiens cDNA FLJ44800 fis, clone BRACE3041162, moderately similar to Homo sapiens zinc finger protein 14 (KOX 6) (ZNF14).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	11952934	11952934	+	IGR	DEL	T	-	-	rs10407228	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11952934delT								ZNF440 (6918 upstream) : ZNF439 (6645 downstream)																																			---	---	---	---
ZNF439	90594	broad.mit.edu	37	19	11973561	11973561	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11973561delT	uc002msr.2	+							NM_152262	NP_689475			zinc finger protein 439						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1																		---	---	---	---
ZNF878	729747	broad.mit.edu	37	19	12157801	12157802	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12157801_12157802insA	uc002mta.1	-							NM_001080404	NP_001073873			zinc finger protein 878						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding				0																		---	---	---	---
ZNF442	79973	broad.mit.edu	37	19	12463795	12463795	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12463795delT	uc002mtr.1	-						ZNF442_uc010xmk.1_Intron	NM_030824	NP_110451			zinc finger protein 442						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(2)|breast(1)|kidney(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	12681696	12681697	+	IGR	INS	-	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12681696_12681697insC								ZNF709 (19340 upstream) : ZNF490 (5223 downstream)																																			---	---	---	---
GCDH	2639	broad.mit.edu	37	19	13001459	13001460	+	5'Flank	DEL	AC	-	-	rs142309574		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13001459_13001460delAC	uc002mvq.2	+						GCDH_uc010xms.1_5'Flank|GCDH_uc002mvp.2_5'Flank|GCDH_uc010xmt.1_5'Flank|GCDH_uc010xmu.1_5'Flank	NM_000159	NP_000150			glutaryl-Coenzyme A dehydrogenase isoform a						lysine catabolic process	mitochondrial matrix	flavin adenine dinucleotide binding|glutaryl-CoA dehydrogenase activity|protein binding				0																		---	---	---	---
SYCE2	256126	broad.mit.edu	37	19	13028934	13028934	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13028934delA	uc002mvr.2	-							NM_001105578	NP_001099048			synaptonemal complex central element protein 2						cell division	central element					0																		---	---	---	---
NACC1	112939	broad.mit.edu	37	19	13248443	13248443	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13248443delT	uc002mwm.2	+							NM_052876	NP_443108			transcriptional repressor NAC1						negative regulation of transcription, DNA-dependent|positive regulation of cell proliferation|protein homooligomerization|transcription, DNA-dependent	cytoplasm|nuclear body					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	13291281	13291281	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13291281delT								IER2 (25565 upstream) : CACNA1A (25975 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	13694932	13694932	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13694932delA								CACNA1A (77658 upstream) : CCDC130 (147642 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	13709248	13709251	+	IGR	DEL	AAGG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13709248_13709251delAAGG								CACNA1A (91974 upstream) : CCDC130 (133323 downstream)																																	OREG0025297	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	19	14041842	14041845	+	IGR	DEL	TTTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14041842_14041845delTTTT								CC2D1A (149 upstream) : PODNL1 (157 downstream)																																			---	---	---	---
LOC113230	113230	broad.mit.edu	37	19	14182141	14182142	+	5'Flank	INS	-	A	A	rs7507971		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14182141_14182142insA	uc002mxz.2	+						LOC113230_uc002mxy.2_5'Flank	NR_024282				RecName: Full=Uncharacterized protein LOC113230;												0																		---	---	---	---
LPHN1	22859	broad.mit.edu	37	19	14277909	14277909	+	Intron	DEL	A	-	-	rs79500350		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14277909delA	uc010xnn.1	-						LPHN1_uc010xno.1_Intron|uc002myf.2_Intron	NM_001008701	NP_001008701			latrophilin 1 isoform 1 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			ovary(2)|lung(2)|central_nervous_system(1)	5																		---	---	---	---
LPHN1	22859	broad.mit.edu	37	19	14278143	14278143	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14278143delG	uc010xnn.1	-						LPHN1_uc010xno.1_Intron|uc002myf.2_Intron	NM_001008701	NP_001008701			latrophilin 1 isoform 1 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			ovary(2)|lung(2)|central_nervous_system(1)	5																		---	---	---	---
PKN1	5585	broad.mit.edu	37	19	14566778	14566780	+	Intron	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14566778_14566780delAAA	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																		---	---	---	---
EMR3	84658	broad.mit.edu	37	19	14762192	14762192	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14762192delA	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																		---	---	---	---
CYP4F22	126410	broad.mit.edu	37	19	15648967	15648967	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15648967delT	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																		---	---	---	---
RAB8A	4218	broad.mit.edu	37	19	16230013	16230013	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16230013delT	uc002ndn.3	+						RAB8A_uc002ndm.1_Intron|RAB8A_uc010xpc.1_Intron	NM_005370	NP_005361			mel transforming oncogene						cilium assembly|Golgi vesicle fusion to target membrane|protein transport|small GTPase mediated signal transduction|vesicle docking involved in exocytosis	Golgi apparatus|nonmotile primary cilium|perinuclear region of cytoplasm|plasma membrane	GTP binding|protein binding			skin(1)	1																		---	---	---	---
RAB8A	4218	broad.mit.edu	37	19	16232381	16232381	+	Intron	DEL	G	-	-	rs112005697		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16232381delG	uc002ndn.3	+						RAB8A_uc002ndm.1_Intron|RAB8A_uc010xpc.1_Intron	NM_005370	NP_005361			mel transforming oncogene						cilium assembly|Golgi vesicle fusion to target membrane|protein transport|small GTPase mediated signal transduction|vesicle docking involved in exocytosis	Golgi apparatus|nonmotile primary cilium|perinuclear region of cytoplasm|plasma membrane	GTP binding|protein binding			skin(1)	1																		---	---	---	---
EPS15L1	58513	broad.mit.edu	37	19	16539362	16539367	+	Intron	DEL	AGAAAG	-	-	rs35804047		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16539362_16539367delAGAAAG	uc002ndz.1	-						EPS15L1_uc002ndx.2_Intron|EPS15L1_uc002ndy.2_Intron|EPS15L1_uc010xpe.1_Intron|EPS15L1_uc010xpf.1_Intron|EPS15L1_uc002nea.1_Intron|EPS15L1_uc010eah.1_Intron|EPS15L1_uc002neb.1_Intron|EPS15L1_uc002nec.1_Intron	NM_021235	NP_067058			epidermal growth factor receptor pathway						endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway	coated pit|nucleus|plasma membrane	calcium ion binding			ovary(3)|skin(2)	5																		---	---	---	---
C19orf44	84167	broad.mit.edu	37	19	16617404	16617404	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16617404delA	uc002neh.1	+						MED26_uc002nee.2_Intron|C19orf44_uc002nef.1_Intron|C19orf44_uc002neg.2_Intron|C19orf44_uc010eai.1_Intron	NM_032207	NP_115583			hypothetical protein LOC84167												0																		---	---	---	---
C19orf42	79086	broad.mit.edu	37	19	16746174	16746175	+	Intron	DEL	AA	-	-	rs34121937		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16746174_16746175delAA	uc002neo.1	-						C19orf42_uc002nep.1_Intron					Homo sapiens cDNA: FLJ21949 fis, clone HEP04922.							integral to membrane					0																		---	---	---	---
F2RL3	9002	broad.mit.edu	37	19	17002568	17002568	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17002568delA	uc002nfa.2	+	2						NM_003950	NP_003941			coagulation factor II (thrombin) receptor-like 3						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|platelet activation|positive regulation of release of sequestered calcium ion into cytosol	extracellular region|integral to plasma membrane	thrombin receptor activity				0																		---	---	---	---
USHBP1	83878	broad.mit.edu	37	19	17369974	17369974	+	Intron	DEL	A	-	-	rs80351288		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17369974delA	uc002nfs.1	-						USHBP1_uc002nfr.1_5'Flank|USHBP1_uc002nft.1_Intron|USHBP1_uc010xpk.1_Intron|USHBP1_uc010eam.1_Intron	NM_031941	NP_114147			Usher syndrome 1C binding protein 1								PDZ domain binding			ovary(1)	1																		---	---	---	---
UNC13A	23025	broad.mit.edu	37	19	17789382	17789382	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17789382delT	uc002nhd.2	-							NM_001080421	NP_001073890			unc-13 homolog A						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	17852989	17852989	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17852989delT								MAP1S (7665 upstream) : FCHO1 (5538 downstream)																																			---	---	---	---
SLC5A5	6528	broad.mit.edu	37	19	17994875	17994875	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17994875delG	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	18161936	18161936	+	IGR	DEL	A	-	-	rs34940946		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18161936delA								ARRDC2 (37031 upstream) : IL12RB1 (8435 downstream)																																			---	---	---	---
PDE4C	5143	broad.mit.edu	37	19	18364361	18364361	+	Intron	DEL	A	-	-	rs35513858		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18364361delA	uc002nil.3	-							NM_000923	NP_000914			phosphodiesterase 4C isoform PDE4C-1						signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(2)|skin(2)|central_nervous_system(1)	5					Dyphylline(DB00651)													---	---	---	---
ZNF90	7643	broad.mit.edu	37	19	20228177	20228178	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20228177_20228178insT	uc002nor.2	+						ZNF90_uc002nos.1_Intron|ZNF90_uc002not.1_Intron	NM_007138	NP_009069			zinc finger protein 90							Golgi apparatus|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	20442752	20442753	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20442752_20442753insT								LOC284441 (72249 upstream) : ZNF826 (8325 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	20672510	20672511	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20672510_20672511insT								ZNF826 (64748 upstream) : ZNF737 (48288 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	22051143	22051143	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22051143delT								ZNF43 (16313 upstream) : ZNF208 (64617 downstream)																																			---	---	---	---
ZNF99	7652	broad.mit.edu	37	19	22952180	22952180	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22952180delT	uc010xrh.1	-							NM_001080409	NP_001073878			zinc finger protein 99											ovary(1)|skin(1)	2		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)																---	---	---	---
Unknown	0	broad.mit.edu	37	19	23261613	23261613	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23261613delT								ZNF99 (308829 upstream) : ZNF91 (259806 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	24542190	24542190	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24542190delT								LOC100101266 (195941 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	28159541	28159541	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28159541delA								None (None upstream) : LOC148189 (121861 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	28401984	28401984	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28401984delG								LOC148189 (117136 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	28447093	28447093	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28447093delT								LOC148189 (162245 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	28754068	28754068	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28754068delT								LOC148189 (469220 upstream) : LOC148145 (701972 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	29315673	29315673	+	IGR	DEL	A	-	-	rs71169791		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29315673delA								None (None upstream) : LOC148145 (140367 downstream)																																			---	---	---	---
C19orf2	8725	broad.mit.edu	37	19	30431543	30431543	+	5'Flank	DEL	A	-	-	rs76450214		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30431543delA	uc002nsr.2	+						C19orf2_uc002nsq.2_Intron|C19orf2_uc002nss.2_5'Flank	NM_003796	NP_003787			RPB5-mediating protein isoform a						protein folding|regulation of transcription from RNA polymerase II promoter|response to virus	DNA-directed RNA polymerase II, core complex|prefoldin complex	transcription corepressor activity|unfolded protein binding			ovary(1)|kidney(1)	2	Ovarian(5;0.000902)|Breast(6;0.0203)|Esophageal squamous(110;0.195)	Hepatocellular(1079;0.137)|Renal(1328;0.228)	STAD - Stomach adenocarcinoma(5;5.36e-06)|Lung(7;0.0144)|LUAD - Lung adenocarcinoma(5;0.115)	STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
C19orf2	8725	broad.mit.edu	37	19	30447914	30447914	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30447914delA	uc002nsr.2	+						C19orf2_uc002nsq.2_Intron|C19orf2_uc002nss.2_Intron	NM_003796	NP_003787			RPB5-mediating protein isoform a						protein folding|regulation of transcription from RNA polymerase II promoter|response to virus	DNA-directed RNA polymerase II, core complex|prefoldin complex	transcription corepressor activity|unfolded protein binding			ovary(1)|kidney(1)	2	Ovarian(5;0.000902)|Breast(6;0.0203)|Esophageal squamous(110;0.195)	Hepatocellular(1079;0.137)|Renal(1328;0.228)	STAD - Stomach adenocarcinoma(5;5.36e-06)|Lung(7;0.0144)|LUAD - Lung adenocarcinoma(5;0.115)	STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
ZNF536	9745	broad.mit.edu	37	19	30957539	30957539	+	Intron	DEL	T	-	-	rs71173907		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30957539delT	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)																	---	---	---	---
ZNF536	9745	broad.mit.edu	37	19	31014594	31014594	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31014594delT	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	31180563	31180563	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31180563delG								ZNF536 (131598 upstream) : DKFZp566F0947 (460220 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	32399236	32399236	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32399236delT								TSHZ3 (559046 upstream) : ZNF507 (437278 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	32480836	32480837	+	IGR	DEL	CA	-	-	rs12610382	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32480836_32480837delCA								TSHZ3 (640646 upstream) : ZNF507 (355677 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	32655656	32655657	+	IGR	INS	-	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32655656_32655657insG								TSHZ3 (815466 upstream) : ZNF507 (180857 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	34094649	34094652	+	IGR	DEL	TGTC	-	-	rs113795313		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34094649_34094652delTGTC								PEPD (81848 upstream) : CHST8 (18209 downstream)																																			---	---	---	---
CHST8	64377	broad.mit.edu	37	19	34139093	34139094	+	Intron	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34139093_34139094delCT	uc002nus.3	+						CHST8_uc002nut.3_Intron	NM_001127895	NP_001121367			carbohydrate (N-acetylgalactosamine 4-0)						carbohydrate biosynthetic process|central nervous system development|hormone biosynthetic process|proteoglycan biosynthetic process|sulfur compound metabolic process	Golgi membrane|integral to membrane	N-acetylgalactosamine 4-O-sulfotransferase activity			skin(2)|large_intestine(1)|ovary(1)	4	Esophageal squamous(110;0.162)																	---	---	---	---
Unknown	0	broad.mit.edu	37	19	34420113	34420113	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34420113delT								KCTD15 (113448 upstream) : LSM14A (243239 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	34434511	34434511	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34434511delC								KCTD15 (127846 upstream) : LSM14A (228841 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	34484672	34484674	+	IGR	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34484672_34484674delAAA								KCTD15 (178007 upstream) : LSM14A (178678 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	34514020	34514021	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34514020_34514021insT								KCTD15 (207355 upstream) : LSM14A (149331 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	34609046	34609047	+	IGR	DEL	GA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34609046_34609047delGA								KCTD15 (302381 upstream) : LSM14A (54305 downstream)																																			---	---	---	---
UBA2	10054	broad.mit.edu	37	19	34925730	34925730	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34925730delT	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)															---	---	---	---
UBA2	10054	broad.mit.edu	37	19	34955943	34955944	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34955943_34955944insA	uc002nvk.2	+						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	35128512	35128512	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35128512delA	uc002nvo.1	-											Homo sapiens cDNA FLJ36176 fis, clone TESTI2026491.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	35343098	35343099	+	RNA	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35343098_35343099delTT	uc002nwk.1	+	5		c.2192_2193delTT								Homo sapiens cDNA FLJ43870 fis, clone TESTI4008219.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	35394166	35394167	+	5'Flank	INS	-	GT	GT			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35394166_35394167insGT	uc002nxe.2	+											Homo sapiens cDNA clone IMAGE:4838482.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	35479971	35479971	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35479971delT								ZNF792 (25018 upstream) : GRAMD1A (5717 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	35686348	35686348	+	IGR	DEL	T	-	-	rs146734337		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35686348delT								FXYD5 (25563 upstream) : FAM187B (29356 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	35893674	35893676	+	5'Flank	DEL	TTT	-	-	rs113227289		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35893674_35893676delTTT	uc002nzf.1	+											Homo sapiens cDNA FLJ46220 fis, clone TESTI4013774.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	36451853	36451853	+	IGR	DEL	T	-	-	rs67179272		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36451853delT								LRFN3 (15758 upstream) : SDHAF1 (34248 downstream)																																			---	---	---	---
ZNF146	7705	broad.mit.edu	37	19	36712639	36712639	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36712639delT	uc002odq.3	+						ZNF146_uc010eet.2_Intron|ZNF146_uc010eeu.2_Intron	NM_007145	NP_009076			zinc finger protein 146						regulation of transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|heparin binding|zinc ion binding				0	Esophageal squamous(110;0.162)																	---	---	---	---
ZNF566	84924	broad.mit.edu	37	19	36981089	36981089	+	5'Flank	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36981089delG	uc002oea.3	-						ZNF566_uc010xte.1_5'Flank|ZNF566_uc010xtf.1_5'Flank|ZNF566_uc002oeb.3_5'Flank|ZNF566_uc002oec.3_5'Flank|ZNF566_uc010xtg.1_5'Flank	NM_032838	NP_116227			zinc finger protein 566 isoform 1						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	37220563	37220564	+	IGR	INS	-	GA	GA			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37220563_37220564insGA								ZNF567 (6315 upstream) : ZNF790 (87769 downstream)																																			---	---	---	---
ZNF585A	199704	broad.mit.edu	37	19	37654164	37654164	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37654164delA	uc002ofo.1	-						ZNF585A_uc002ofm.1_Intron|ZNF585A_uc002ofn.1_Intron	NM_199126	NP_954577			zinc finger protein 585A						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
HKR1	284459	broad.mit.edu	37	19	37814063	37814063	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37814063delT	uc002ofx.2	+						HKR1_uc002ofy.2_Intron					SubName: Full=HKR1 protein;						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
SIPA1L3	23094	broad.mit.edu	37	19	38469853	38469853	+	Intron	DEL	A	-	-	rs34849437		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38469853delA	uc002ohk.2	+							NM_015073	NP_055888			signal-induced proliferation-associated 1 like						regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)															---	---	---	---
FBXO17	115290	broad.mit.edu	37	19	39442159	39442161	+	Intron	DEL	AAA	-	-	rs34437526		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39442159_39442161delAAA	uc002okg.1	-						SARS2_uc010xuq.1_5'Flank|FBXO17_uc002okf.1_Intron	NM_024907	NP_079183			F-box protein FBG4 isoform 2						protein catabolic process	SCF ubiquitin ligase complex	glycoprotein binding				0	all_cancers(60;8.37e-07)|all_lung(34;3.71e-07)|Lung NSC(34;4.17e-07)|all_epithelial(25;1.13e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)															---	---	---	---
PAK4	10298	broad.mit.edu	37	19	39614497	39614500	+	5'Flank	DEL	GAAG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39614497_39614500delGAAG	uc002okj.1	+						PAK4_uc002okl.1_5'Flank|PAK4_uc002okn.1_5'Flank|PAK4_uc002okm.1_5'Flank|PAK4_uc002oko.1_5'Flank|PAK4_uc002okp.1_5'Flank	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	39667515	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39667515delT	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)															---	---	---	---
SYCN	342898	broad.mit.edu	37	19	39696146	39696146	+	5'Flank	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39696146delA	uc002okr.2	-							NM_001080468	NP_001073937			syncollin precursor						exocytosis	transport vesicle membrane					0	all_cancers(60;7.32e-07)|all_lung(34;1.58e-07)|Lung NSC(34;1.88e-07)|all_epithelial(25;8.97e-07)|Ovarian(47;0.0454)		Epithelial(26;1.34e-25)|all cancers(26;9.31e-23)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	39792222	39792223	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39792222_39792223delAA								IL29 (2911 upstream) : LRFN1 (5234 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	40253156	40253156	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40253156delA								CLC (24488 upstream) : LEUTX (14078 downstream)																																			---	---	---	---
FCGBP	8857	broad.mit.edu	37	19	40419370	40419370	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40419370delA	uc002omp.3	-							NM_003890	NP_003881			Fc fragment of IgG binding protein precursor							extracellular region	protein binding			ovary(4)|skin(4)|central_nervous_system(1)	9	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)															---	---	---	---
SPTBN4	57731	broad.mit.edu	37	19	41030420	41030420	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41030420delA	uc002ony.2	+						SPTBN4_uc002onx.2_Intron|SPTBN4_uc002onz.2_Intron|SPTBN4_uc010egx.2_Intron	NM_020971	NP_066022			spectrin, beta, non-erythrocytic 4 isoform						actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(1)|skin(1)	5			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	41164538	41164539	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41164538_41164539delTT								LTBP4 (28813 upstream) : NUMBL (7275 downstream)																																			---	---	---	---
EGLN2	112398	broad.mit.edu	37	19	41305794	41305797	+	Intron	DEL	TCTG	-	-	rs111833532		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41305794_41305797delTCTG	uc010ehd.2	+						EGLN2_uc002opg.3_Intron|EGLN2_uc002oph.2_Intron|EGLN2_uc002opi.2_5'Flank	NM_080732	NP_542770			EGL nine (C.elegans) homolog 2						cell redox homeostasis|estrogen receptor signaling pathway|positive regulation of protein catabolic process|regulation of cell growth|response to hypoxia	cytoplasm|nucleus	ferrous iron binding|L-ascorbic acid binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|oxygen sensor activity			ovary(2)	2			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Vitamin C(DB00126)													---	---	---	---
CYP2A7	1549	broad.mit.edu	37	19	41448329	41448330	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41448329_41448330delTT	uc002opo.2	-						CYP2B7P1_uc002opq.2_Intron	NM_000764	NP_000755			cytochrome P450, family 2, subfamily A,							endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	42144076	42144076	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42144076delC								CEACAM4 (10634 upstream) : CEACAM7 (33159 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	42293713	42293714	+	IGR	INS	-	AAGG	AAGG	rs71870163		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42293713_42293714insAAGG								CEACAM6 (17600 upstream) : CEACAM3 (6820 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	42294708	42294709	+	IGR	INS	-	AT	AT	rs149438257	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42294708_42294709insAT								CEACAM6 (18595 upstream) : CEACAM3 (5825 downstream)																																			---	---	---	---
ZNF574	64763	broad.mit.edu	37	19	42570626	42570629	+	5'Flank	DEL	AAAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42570626_42570629delAAAA	uc002osk.3	+						GRIK5_uc002osj.1_5'Flank|GRIK5_uc010eib.1_5'Flank	NM_022752	NP_073589			zinc finger protein 574						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.059)																---	---	---	---
MEGF8	1954	broad.mit.edu	37	19	42864447	42864447	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42864447delT	uc002otl.3	+						MEGF8_uc002otm.3_Intron	NM_001410	NP_001401			multiple EGF-like-domains 8							integral to membrane	calcium ion binding|structural molecule activity			ovary(1)	1		Prostate(69;0.00682)																---	---	---	---
CEACAM1	634	broad.mit.edu	37	19	43016797	43016797	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43016797delT	uc002otv.2	-						uc010eif.1_Intron|uc002ott.1_Intron|uc010eig.1_Intron|uc010eih.1_Intron|CEACAM1_uc010eii.2_Intron|CEACAM1_uc002otw.2_Intron|CEACAM1_uc010eij.2_Intron|CEACAM1_uc002otx.2_Intron|CEACAM1_uc002oty.2_Intron|CEACAM1_uc002otz.2_Intron|CEACAM1_uc010eik.2_Intron	NM_001712	NP_001703			carcinoembryonic antigen-related cell adhesion						angiogenesis|cell migration|homophilic cell adhesion|integrin-mediated signaling pathway	extracellular region|integral to plasma membrane|membrane fraction				ovary(1)|central_nervous_system(1)	2		Prostate(69;0.00682)		GBM - Glioblastoma multiforme(486;0.00148)	Arcitumomab(DB00113)													---	---	---	---
PLAUR	5329	broad.mit.edu	37	19	44166873	44166877	+	Intron	DEL	TTTTT	-	-	rs112075151		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44166873_44166877delTTTTT	uc002oxf.1	-						PLAUR_uc002oxd.1_Intron|PLAUR_uc002oxe.1_Intron|PLAUR_uc002oxg.1_Intron	NM_002659	NP_002650			plasminogen activator, urokinase receptor						attachment of GPI anchor to protein|blood coagulation|C-terminal protein lipidation|cellular component movement|chemotaxis|fibrinolysis|regulation of proteolysis	anchored to membrane|cell surface|endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region|extrinsic to membrane|integral to membrane|plasma membrane	enzyme binding|U-plasminogen activator receptor activity			ovary(1)	1		Prostate(69;0.0153)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Urokinase(DB00013)													---	---	---	---
ZNF404	342908	broad.mit.edu	37	19	44378950	44378950	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44378950delT	uc002oxs.3	-							NM_001033719	NP_001028891			zinc finger protein 404						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0352)																---	---	---	---
ZNF233	353355	broad.mit.edu	37	19	44776905	44776905	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44776905delA	uc002oyz.1	+						ZNF235_uc002oyx.1_Intron|ZNF235_uc010eji.2_Intron|ZNF233_uc002oyy.1_Intron	NM_181756	NP_861421			zinc finger protein 233						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)	2		Prostate(69;0.0435)|all_neural(266;0.226)																---	---	---	---
Unknown	0	broad.mit.edu	37	19	44819606	44819606	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44819606delT								ZNF235 (10428 upstream) : ZFP112 (11101 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	45194076	45194077	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45194076_45194077delAA								CEACAM19 (6451 upstream) : CEACAM16 (8281 downstream)																																			---	---	---	---
CBLC	23624	broad.mit.edu	37	19	45284934	45284934	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45284934delG	uc002ozs.2	+						CBLC_uc010ejt.2_Intron	NM_012116	NP_036248			Cas-Br-M (murine) ecotropic retroviral						cell surface receptor linked signaling pathway|negative regulation of epidermal growth factor receptor activity|negative regulation of MAP kinase activity|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	calcium ion binding|epidermal growth factor receptor binding|phosphotyrosine binding|SH3 domain binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(1)|skin(1)	6	Lung NSC(12;0.00136)|all_lung(12;0.00371)	Ovarian(192;0.231)						M		AML								---	---	---	---
CBLC	23624	broad.mit.edu	37	19	45294565	45294565	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45294565delA	uc002ozs.2	+						CBLC_uc010ejt.2_Intron	NM_012116	NP_036248			Cas-Br-M (murine) ecotropic retroviral						cell surface receptor linked signaling pathway|negative regulation of epidermal growth factor receptor activity|negative regulation of MAP kinase activity|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	calcium ion binding|epidermal growth factor receptor binding|phosphotyrosine binding|SH3 domain binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(1)|skin(1)	6	Lung NSC(12;0.00136)|all_lung(12;0.00371)	Ovarian(192;0.231)						M		AML								---	---	---	---
APOC1	341	broad.mit.edu	37	19	45419666	45419666	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45419666delA	uc002pac.1	+						APOC1_uc002pad.1_Intron|APOC1_uc002pae.1_Intron|APOC1_uc002paf.1_Intron	NM_001645	NP_001636			apolipoprotein C-I precursor						cholesterol efflux|chylomicron remnant clearance|high-density lipoprotein particle remodeling|lipoprotein metabolic process|negative regulation of cholesterol transport|negative regulation of fatty acid biosynthetic process|negative regulation of lipoprotein lipase activity|negative regulation of phosphatidylcholine catabolic process|negative regulation of receptor-mediated endocytosis|negative regulation of very-low-density lipoprotein particle clearance|phospholipid efflux|positive regulation of cholesterol esterification|very-low-density lipoprotein particle assembly|very-low-density lipoprotein particle clearance	chylomicron|endoplasmic reticulum|high-density lipoprotein particle|very-low-density lipoprotein particle	fatty acid binding|phosphatidylcholine binding|phosphatidylcholine-sterol O-acyltransferase activator activity|phospholipase inhibitor activity				0	Lung NSC(12;0.0018)|all_lung(12;0.00481)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00327)|Epithelial(262;0.174)														---	---	---	---
APOC1P1	342	broad.mit.edu	37	19	45431268	45431268	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45431268delA	uc010eju.2	+											Homo sapiens clone DKFZp781C1677 mRNA sequence.												0																		---	---	---	---
APOC2	344	broad.mit.edu	37	19	45452308	45452309	+	Intron	INS	-	TCT	TCT			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45452308_45452309insTCT	uc002pah.2	+							NM_000483	NP_000474			apolipoprotein C-II precursor						cholesterol efflux|chylomicron remnant clearance|high-density lipoprotein particle clearance|lipid catabolic process|lipoprotein metabolic process|negative regulation of cholesterol transport|negative regulation of lipid metabolic process|negative regulation of receptor-mediated endocytosis|negative regulation of very-low-density lipoprotein particle clearance|phospholipid efflux|positive regulation of fatty acid biosynthetic process|positive regulation of lipoprotein lipase activity|positive regulation of phospholipase activity|positive regulation of phospholipid catabolic process|positive regulation of triglyceride catabolic process|triglyceride homeostasis|very-low-density lipoprotein particle remodeling	chylomicron|intermediate-density lipoprotein particle|low-density lipoprotein particle|spherical high-density lipoprotein particle|very-low-density lipoprotein particle	lipase inhibitor activity|lipid binding|lipoprotein lipase activator activity|phospholipase activator activity|phospholipase binding|protein homodimerization activity			kidney(1)	1	Lung NSC(12;0.00858)|all_lung(12;0.0197)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00327)|Epithelial(262;0.174)														---	---	---	---
SFRS16	11129	broad.mit.edu	37	19	45565044	45565046	+	Intron	DEL	ATC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45565044_45565046delATC	uc002pak.2	+						SFRS16_uc002pal.2_Intron|SFRS16_uc010xxh.1_Intron|SFRS16_uc002pam.2_Intron|SFRS16_uc002pan.1_Intron	NM_007056	NP_008987			splicing factor, arginine/serine-rich 16						mRNA processing|RNA splicing	nucleus					0		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0102)														---	---	---	---
GPR4	2828	broad.mit.edu	37	19	46108129	46108129	+	5'Flank	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46108129delA	uc002pcm.2	-						OPA3_uc010xxk.1_5'Flank	NM_005282	NP_005273			G protein-coupled receptor 4							integral to plasma membrane	G-protein coupled receptor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(262;0.0071)|GBM - Glioblastoma multiforme(486;0.128)|Epithelial(262;0.223)														---	---	---	---
EML2	24139	broad.mit.edu	37	19	46118884	46118884	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46118884delA	uc002pcn.2	-						EML2_uc002pco.2_Intron|EML2_uc002pcp.2_Intron|EML2_uc010xxl.1_Intron|EML2_uc010xxm.1_Intron	NM_012155	NP_036287			echinoderm microtubule associated protein like						sensory perception of sound|visual perception	cytoplasm|intracellular membrane-bounded organelle|microtubule|microtubule associated complex	catalytic activity|protein binding			large_intestine(1)|ovary(1)	2		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)														---	---	---	---
EML2	24139	broad.mit.edu	37	19	46132083	46132086	+	Intron	DEL	AAGT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46132083_46132086delAAGT	uc002pcn.2	-						EML2_uc002pco.2_Intron|EML2_uc002pcp.2_Intron|EML2_uc010xxl.1_Intron|EML2_uc010xxm.1_Intron|EML2_uc010xxn.1_Intron|EML2_uc010xxo.1_Intron|EML2_uc010ekj.2_Intron|EML2_uc010ekk.1_Intron	NM_012155	NP_036287			echinoderm microtubule associated protein like						sensory perception of sound|visual perception	cytoplasm|intracellular membrane-bounded organelle|microtubule|microtubule associated complex	catalytic activity|protein binding			large_intestine(1)|ovary(1)	2		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)														---	---	---	---
IRF2BP1	26145	broad.mit.edu	37	19	46389747	46389747	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46389747delT	uc002pds.1	-							NM_015649	NP_056464			interferon regulatory factor 2 binding protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00442)|GBM - Glioblastoma multiforme(486;0.0402)|Epithelial(262;0.231)														---	---	---	---
GRLF1	2909	broad.mit.edu	37	19	47464151	47464154	+	Intron	DEL	TTTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47464151_47464154delTTTT	uc010ekv.2	+							NM_004491	NP_004482			glucocorticoid receptor DNA binding factor 1						axon guidance|negative regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol	DNA binding|Rho GTPase activator activity|transcription corepressor activity			central_nervous_system(1)	1		all_cancers(25;1.51e-09)|all_epithelial(76;1.87e-07)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|Ovarian(192;0.0129)|all_neural(266;0.026)|Breast(70;0.077)		all cancers(93;2.03e-05)|OV - Ovarian serous cystadenocarcinoma(262;2.57e-05)|Epithelial(262;0.00135)|GBM - Glioblastoma multiforme(486;0.0289)														---	---	---	---
CCDC9	26093	broad.mit.edu	37	19	47774982	47775001	+	3'UTR	DEL	GTGTGTGTGCGCGCGCGCGC	-	-	rs58160287	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47774982_47775001delGTGTGTGTGCGCGCGCGCGC	uc010xym.1	+	12						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)														---	---	---	---
C5AR1	728	broad.mit.edu	37	19	47819706	47819708	+	Intron	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47819706_47819708delTTT	uc002pgj.1	+							NM_001736	NP_001727			complement component 5 receptor 1						activation of MAPK activity|activation of phospholipase C activity|cellular defense response|elevation of cytosolic calcium ion concentration|immune response|sensory perception of chemical stimulus	integral to plasma membrane	C5a anaphylatoxin receptor activity			ovary(2)|central_nervous_system(1)|skin(1)	4		all_cancers(25;2e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;0.000267)|OV - Ovarian serous cystadenocarcinoma(262;0.000618)|Epithelial(262;0.0142)|GBM - Glioblastoma multiforme(486;0.0242)														---	---	---	---
MEIS3	56917	broad.mit.edu	37	19	47910236	47910236	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47910236delG	uc002pgu.2	-						MEIS3_uc010xyp.1_Intron|MEIS3_uc002pgo.2_Intron|MEIS3_uc002pgp.2_Intron|MEIS3_uc002pgq.2_Intron|MEIS3_uc002pgr.2_Intron|MEIS3_uc002pgt.2_Intron|MEIS3_uc002pgv.2_Intron|MEIS3_uc002pgs.2_Intron|MEIS3_uc010eld.2_Intron	NM_001009813	NP_001009813			Meis1, myeloid ecotropic viral integration site							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;0.000198)|OV - Ovarian serous cystadenocarcinoma(262;0.000439)|Epithelial(262;0.0113)|GBM - Glioblastoma multiforme(486;0.0223)														---	---	---	---
ZNF541	84215	broad.mit.edu	37	19	48026347	48026347	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48026347delT	uc010xyt.1	-						ZNF541_uc002phg.3_Intron|ZNF541_uc010elh.2_Intron|ZNF541_uc010eli.2_Intron	NM_001101419	NP_001094889			zinc finger protein 541						cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1																		---	---	---	---
ZNF541	84215	broad.mit.edu	37	19	48043661	48043661	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48043661delT	uc010xyt.1	-						ZNF541_uc002phg.3_Intron|ZNF541_uc010elh.2_Intron|ZNF541_uc010eli.2_Intron	NM_001101419	NP_001094889			zinc finger protein 541						cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	48687210	48687210	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48687210delT	uc002pic.3	+											RecName: Full=Uncharacterized protein C19orf68;																														---	---	---	---
GRIN2D	2906	broad.mit.edu	37	19	48943858	48943858	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48943858delA	uc002pjc.3	+						GRIN2D_uc010elx.2_Intron	NM_000836	NP_000827			N-methyl-D-aspartate receptor subunit 2D							cell junction|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|protein binding			ovary(3)|breast(3)	6		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Orphenadrine(DB01173)													---	---	---	---
RUVBL2	10856	broad.mit.edu	37	19	49499408	49499408	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49499408delA	uc002plr.1	+						GYS1_uc010xzy.1_5'Flank|GYS1_uc002plp.2_5'Flank|GYS1_uc010emm.2_5'Flank|GYS1_uc010xzz.1_5'Flank|GYS1_uc010yaa.1_5'Flank|RUVBL2_uc002plq.1_Intron|RUVBL2_uc010yab.1_Intron|RUVBL2_uc002pls.1_Intron|RUVBL2_uc010emn.1_Intron|RUVBL2_uc010yac.1_Intron	NM_006666	NP_006657			RuvB-like 2						cellular response to UV|DNA recombination|DNA repair|histone H2A acetylation|histone H4 acetylation|protein folding|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|Ino80 complex|membrane|MLL1 complex|NuA4 histone acetyltransferase complex|nuclear matrix	ATP binding|ATP-dependent DNA helicase activity|damaged DNA binding|identical protein binding|unfolded protein binding				0		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000449)|OV - Ovarian serous cystadenocarcinoma(262;0.000555)|GBM - Glioblastoma multiforme(486;0.00585)|Epithelial(262;0.047)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	49746340	49746341	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49746340_49746341delTT								TRPM4 (31249 upstream) : SLC6A16 (46553 downstream)																																			---	---	---	---
CCDC155	147872	broad.mit.edu	37	19	49901949	49901950	+	Intron	INS	-	CT	CT	rs139893707	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49901949_49901950insCT	uc002pnm.1	+						CCDC155_uc002pnl.1_Intron|CCDC155_uc010emx.1_Intron	NM_144688	NP_653289			coiled-coil domain containing 155							integral to membrane	calcium ion binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
CPT1C	126129	broad.mit.edu	37	19	50215900	50215900	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50215900delA	uc002ppj.2	+						CPT1C_uc002ppi.2_Intron|CPT1C_uc002ppk.2_Intron|CPT1C_uc010eng.2_Intron|CPT1C_uc010enh.2_Intron|CPT1C_uc010eni.1_Intron	NM_152359	NP_689572			carnitine palmitoyltransferase 1C isoform 2						fatty acid metabolic process	integral to membrane|mitochondrial outer membrane	carnitine O-palmitoyltransferase activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0011)|GBM - Glioblastoma multiforme(134;0.00786)														---	---	---	---
MYH14	79784	broad.mit.edu	37	19	50738305	50738307	+	Intron	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50738305_50738307delAAA	uc002prr.1	+						MYH14_uc010enu.1_Intron|MYH14_uc002prq.1_Intron	NM_024729	NP_079005			myosin, heavy chain 14 isoform 2						axon guidance|regulation of cell shape	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(1)	1		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)														---	---	---	---
KLK3	354	broad.mit.edu	37	19	51355433	51355433	+	5'Flank	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51355433delG	uc002pts.1	+						KLK3_uc002ptp.1_5'Flank|KLK3_uc010ycj.1_5'Flank|KLK3_uc002ptr.1_5'Flank|KLK3_uc010eof.1_5'Flank	NM_001030047	NP_001025218			prostate specific antigen isoform 3						negative regulation of angiogenesis|proteolysis	extracellular region	serine-type endopeptidase activity			upper_aerodigestive_tract(1)|ovary(1)|kidney(1)	3		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00763)|GBM - Glioblastoma multiforme(134;0.0144)														---	---	---	---
VSIG10L	147645	broad.mit.edu	37	19	51836784	51836786	+	Intron	DEL	AAA	-	-	rs72135418		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51836784_51836786delAAA	uc002pwf.2	-						VSIG10L_uc002pwd.2_Intron	NM_001163922	NP_001157394			V-set and immunoglobulin domain containing 10							integral to membrane					0																		---	---	---	---
ZNF577	84765	broad.mit.edu	37	19	52383660	52383660	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52383660delA	uc010yde.1	-						ZNF577_uc010ydd.1_Intron|ZNF577_uc002pxx.3_Intron|ZNF577_uc002pxv.2_Intron|ZNF577_uc002pxw.2_Intron	NM_032679	NP_116068			zinc finger protein 577 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)														---	---	---	---
ZNF616	90317	broad.mit.edu	37	19	52639703	52639703	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52639703delA	uc002pym.2	-						ZNF616_uc002pyn.2_Intron	NM_178523	NP_848618			zinc finger protein 616						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00392)|OV - Ovarian serous cystadenocarcinoma(262;0.0189)														---	---	---	---
ZNF816A	125893	broad.mit.edu	37	19	53455153	53455153	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53455153delA	uc002qal.1	-						ZNF321_uc010eqj.2_Intron|ZNF321_uc002qak.1_Intron|ZNF816A_uc002qam.1_Intron	NM_001031665	NP_001026835			zinc finger protein 816A						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.0313)														---	---	---	---
ZNF765	91661	broad.mit.edu	37	19	53868298	53868298	+	5'Flank	DEL	A	-	-	rs34263503		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53868298delA	uc010ydx.1	+						ZNF525_uc010eqn.2_5'Flank|ZNF525_uc002qbl.2_5'Flank	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	54115338	54115339	+	IGR	DEL	AA	-	-	rs76272236		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54115338_54115339delAA								LOC284379 (8587 upstream) : DPRX (19971 downstream)																																			---	---	---	---
MIR518E	574487	broad.mit.edu	37	19	54232896	54232897	+	5'Flank	INS	-	AGA	AGA			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54232896_54232897insAGA	hsa-mir-518e|MI0003169	+						MIR518A1_hsa-mir-518a-1|MI0003170_5'Flank																	0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	54279184	54279184	+	IGR	DEL	T	-	-	rs62146188		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54279184delT								MIR519A2 (13500 upstream) : MIR371 (11745 downstream)																																			---	---	---	---
PRKCG	5582	broad.mit.edu	37	19	54409789	54409789	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54409789delG	uc002qcq.1	+						PRKCG_uc010yeg.1_Intron|PRKCG_uc010yeh.1_Intron	NM_002739	NP_002730			protein kinase C, gamma						activation of phospholipase C activity|cell death|intracellular signal transduction|negative regulation of protein catabolic process|negative regulation of protein ubiquitination|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of mismatch repair|synaptic transmission	cytosol	ATP binding|protein kinase C activity|zinc ion binding			lung(4)|ovary(2)|pancreas(2)|large_intestine(1)	9	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)												OREG0025667	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CACNG8	59283	broad.mit.edu	37	19	54482863	54482864	+	Intron	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54482863_54482864delAG	uc002qcs.1	+						MIR935_hsa-mir-935|MI0005757_5'Flank	NM_031895	NP_114101			voltage-dependent calcium channel gamma-8						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|cell junction|endocytic vesicle membrane|postsynaptic density|postsynaptic membrane|voltage-gated calcium channel complex	voltage-gated calcium channel activity				0	all_cancers(19;0.0385)|all_epithelial(19;0.0207)|all_lung(19;0.145)|Lung NSC(19;0.168)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.162)														---	---	---	---
TFPT	29844	broad.mit.edu	37	19	54614085	54614085	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54614085delA	uc010yej.1	-						TFPT_uc010erd.2_Intron	NM_013342	NP_037474			TCF3 (E2A) fusion partner						apoptosis|DNA recombination|DNA repair|induction of apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|Ino80 complex	DNA binding|protein binding				0	all_cancers(19;0.004)|all_epithelial(19;0.00195)|all_lung(19;0.0193)|Lung NSC(19;0.0358)|Breast(117;0.137)|Ovarian(34;0.19)							T	TCF3	pre-B ALL								---	---	---	---
KIR2DL1	3802	broad.mit.edu	37	19	55286500	55286501	+	Intron	DEL	GA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55286500_55286501delGA	uc002qhb.1	+						KIR2DS4_uc010yfj.1_Intron|KIR2DS4_uc010yfk.1_Intron|KIR2DL3_uc010erw.1_Intron|KIR2DL1_uc002qgz.1_Intron|KIR2DL3_uc002qha.1_Intron|KIR3DP1_uc010yfi.1_Intron|KIR2DL1_uc010erz.1_Intron	NM_014218	NP_055033			killer cell immunoglobulin-like receptor, two						immune response|natural killer cell inhibitory signaling pathway	integral to plasma membrane	protein binding|receptor activity				0				GBM - Glioblastoma multiforme(193;0.0192)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	55402859	55402859	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55402859delT								FCAR (1021 upstream) : NCR1 (14649 downstream)																																			---	---	---	---
NLRP7	199713	broad.mit.edu	37	19	55464454	55464454	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55464454delA	uc010esl.2	-							NM_001127255	NP_001120727			NACHT, leucine rich repeat and PYD containing 7								ATP binding			large_intestine(1)|breast(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(193;0.0325)														---	---	---	---
HSPBP1	23640	broad.mit.edu	37	19	55777911	55777912	+	Intron	INS	-	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55777911_55777912insC	uc002qjx.2	-						HSPBP1_uc002qjy.2_Intron|HSPBP1_uc002qkb.2_Intron|HSPBP1_uc002qka.2_Intron|HSPBP1_uc002qkd.2_Intron|HSPBP1_uc002qkc.2_Intron|uc002qke.2_5'Flank	NM_012267	NP_036399			hsp70-interacting protein						positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein folding		enzyme inhibitor activity|protein binding				0			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0452)														---	---	---	---
TMEM150B	284417	broad.mit.edu	37	19	55840148	55840148	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55840148delA	uc002qki.2	-							NM_001085488	NP_001078957			transmembrane protein 150B precursor							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	56641422	56641422	+	IGR	DEL	A	-	-	rs113879418		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56641422delA								ZNF787 (8773 upstream) : ZNF444 (11134 downstream)																																			---	---	---	---
ZSCAN5A	79149	broad.mit.edu	37	19	56755276	56755276	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56755276delT	uc002qmr.2	-						ZSCAN5A_uc010ygi.1_Intron	NM_024303	NP_077279			zinc finger and SCAN domain containing 5A						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3																		---	---	---	---
ZNF667	63934	broad.mit.edu	37	19	56985397	56985397	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56985397delT	uc002qnd.2	-						ZNF667_uc010etl.2_5'Flank|ZNF667_uc002qne.2_5'UTR|ZNF667_uc010etm.2_Intron	NM_022103	NP_071386			zinc finger protein 667						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)														---	---	---	---
ZNF471	57573	broad.mit.edu	37	19	57029835	57029835	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57029835delT	uc002qnh.2	+							NM_020813	NP_065864			zinc finger protein 471						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0307)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	57251698	57251698	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57251698delT	uc010ygp.1	+											Homo sapiens cDNA clone IMAGE:4793694.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	57266848	57266848	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57266848delT	uc010ygp.1	+											Homo sapiens cDNA clone IMAGE:4793694.																														---	---	---	---
USP29	57663	broad.mit.edu	37	19	57639426	57639427	+	Intron	INS	-	C	C	rs140354682	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57639426_57639427insC	uc002qny.2	+							NM_020903	NP_065954			ubiquitin specific peptidase 29						protein modification process|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|protein binding|ubiquitin thiolesterase activity			lung(6)|ovary(2)|breast(2)|pancreas(1)	11		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)														---	---	---	---
ZNF264	9422	broad.mit.edu	37	19	57725719	57725720	+	3'UTR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57725719_57725720insT	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)														---	---	---	---
AURKC	6795	broad.mit.edu	37	19	57745123	57745123	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57745123delT	uc002qoe.2	+						AURKC_uc002qoc.2_Intron|AURKC_uc002qod.2_Intron|AURKC_uc010etv.2_Intron	NM_001015878	NP_001015878			aurora kinase C isoform 1						cell cycle|cytokinesis	condensed chromosome|cytoplasm|midbody|spindle midzone	ATP binding|protein serine/threonine kinase activity			lung(4)|ovary(2)	6		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0122)														---	---	---	---
ZNF329	79673	broad.mit.edu	37	19	58652533	58652533	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58652533delT	uc002qrn.2	-						ZNF329_uc010euk.1_Intron|ZNF329_uc002qro.1_Intron|ZNF329_uc002qrp.1_Intron	NM_024620	NP_078896			zinc finger protein 329						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.029)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.017)|Lung(386;0.216)														---	---	---	---
ZNF274	10782	broad.mit.edu	37	19	58723422	58723422	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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)														---	---	---	---
ZNF324B	388569	broad.mit.edu	37	19	58963456	58963456	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58963456delG	uc002qsv.1	+						ZNF324B_uc002qsu.1_Intron|ZNF324B_uc010euq.1_Intron	NM_207395	NP_997278			zinc finger protein 324B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)														---	---	---	---
CHMP2A	27243	broad.mit.edu	37	19	59064429	59064430	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:59064429_59064430delTT	uc002qti.2	-						CHMP2A_uc002qtj.2_Intron|CHMP2A_uc002qtk.2_Intron	NM_198426	NP_940818			chromatin modifying protein 2A						cellular membrane organization|endosome transport|protein transport	cytosol|late endosome membrane	protein domain specific binding				0		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)														---	---	---	---
Unknown	0	broad.mit.edu	37	20	195438	195438	+	IGR	DEL	T	-	-	rs112809391		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:195438delT								DEFB128 (25174 upstream) : DEFB129 (12487 downstream)																																			---	---	---	---
SRXN1	140809	broad.mit.edu	37	20	640024	640025	+	Intron	INS	-	GGAG	GGAG	rs147132644	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:640024_640025insGGAG	uc002web.2	-											Homo sapiens full length insert cDNA YO23H03.						response to oxidative stress	cytosol	antioxidant activity|ATP binding|DNA binding|sulfiredoxin activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	680420	680420	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:680420delG								SRXN1 (23597 upstream) : C20orf54 (60305 downstream)																																			---	---	---	---
PSMF1	9491	broad.mit.edu	37	20	1120719	1120719	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1120719delT	uc002wel.3	+						PSMF1_uc010zpo.1_Intron|PSMF1_uc002wem.3_Intron|PSMF1_uc010zpp.1_Intron|PSMF1_uc002wen.3_Intron|PSMF1_uc002wep.3_Intron	NM_178578	NP_848693			proteasome inhibitor subunit 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome core complex	endopeptidase inhibitor activity|protein binding				0																		---	---	---	---
SIRPA	140885	broad.mit.edu	37	20	1914956	1914956	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1914956delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	20	2221933	2221936	+	IGR	DEL	CTTT	-	-	rs112657934		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2221933_2221936delCTTT								STK35 (92737 upstream) : TGM3 (54677 downstream)																																			---	---	---	---
PTPRA	5786	broad.mit.edu	37	20	2898449	2898449	+	Intron	DEL	A	-	-	rs76164519		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2898449delA	uc010zqb.1	+						VPS16_uc002whh.2_Intron|PTPRA_uc002whj.2_Intron|PTPRA_uc010zqc.1_Intron|PTPRA_uc002whk.2_Intron|PTPRA_uc010zqd.1_Intron|PTPRA_uc002whl.2_Intron|PTPRA_uc002whm.2_Intron					SubName: Full=cDNA FLJ60525, highly similar to Receptor-type tyrosine-protein phosphatase alpha (EC 3.1.3.48);						axon guidance|protein phosphorylation	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
UBOX5	22888	broad.mit.edu	37	20	3121540	3121540	+	Intron	DEL	T	-	-	rs11365727		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3121540delT	uc002whw.2	-						uc002whv.1_Intron|UBOX5_uc002whx.2_Intron|UBOX5_uc002why.1_Intron	NM_014948	NP_055763			U-box domain containing 5 isoform a							nucleus|ubiquitin ligase complex	ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
ATRN	8455	broad.mit.edu	37	20	3565278	3565278	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3565278delT	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																		---	---	---	---
PANK2	80025	broad.mit.edu	37	20	3880683	3880683	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3880683delT	uc002wkc.2	+						PANK2_uc002wkb.2_Intron|PANK2_uc010gbd.1_Intron|PANK2_uc002wkd.2_Intron|PANK2_uc002wke.2_Intron|PANK2_uc002wkf.2_Intron	NM_153638	NP_705902			pantothenate kinase 2 isoform 1 preproprotein						cell death|coenzyme A biosynthetic process|pantothenate metabolic process	mitochondrial intermembrane space|nucleus	ATP binding|pantothenate kinase activity|protein binding				0																		---	---	---	---
RNF24	11237	broad.mit.edu	37	20	3922258	3922258	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3922258delA	uc002wkh.2	-						RNF24_uc002wki.2_Intron|RNF24_uc002wkj.2_Intron	NM_007219	NP_009150			ring finger protein 24 isoform 1							Golgi membrane|integral to membrane	zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	4272302	4272302	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4272302delT								ADRA1D (42643 upstream) : PRNP (394495 downstream)																																			---	---	---	---
RASSF2	9770	broad.mit.edu	37	20	4794429	4794430	+	Intron	DEL	GT	-	-	rs11468773		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4794429_4794430delGT	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																		---	---	---	---
C20orf30	29058	broad.mit.edu	37	20	5066349	5066349	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5066349delA	uc010gbi.2	-							NM_014145	NP_054864			hypothetical protein LOC29058 isoform 2							integral to membrane					0																		---	---	---	---
GPCPD1	56261	broad.mit.edu	37	20	5560818	5560818	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5560818delT	uc002wme.3	-						GPCPD1_uc002wmd.3_Intron	NM_019593	NP_062539			hypothetical protein LOC56261						glycerol metabolic process|lipid metabolic process		carbohydrate binding|glycerophosphodiester phosphodiesterase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	6621593	6621593	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6621593delA								FERMT1 (517402 upstream) : BMP2 (127152 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	6973975	6973976	+	IGR	INS	-	AG	AG			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6973975_6973976insAG								BMP2 (213065 upstream) : HAO1 (889655 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	7677076	7677076	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7677076delT								BMP2 (916166 upstream) : HAO1 (186555 downstream)																																			---	---	---	---
HAO1	54363	broad.mit.edu	37	20	7914089	7914089	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7914089delT	uc002wmw.1	-						HAO1_uc010gbu.2_Intron	NM_017545	NP_060015			hydroxyacid oxidase 1						cellular nitrogen compound metabolic process|fatty acid alpha-oxidation|glycolate catabolic process|glyoxylate metabolic process	peroxisomal matrix	FMN binding|glycolate oxidase activity|glyoxylate oxidase activity			ovary(3)	3																		---	---	---	---
PLCB1	23236	broad.mit.edu	37	20	8255129	8255129	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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																		---	---	---	---
PLCB1	23236	broad.mit.edu	37	20	8260983	8260985	+	Intron	DEL	AAA	-	-	rs74960469		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8260983_8260985delAAA	uc002wnb.2	+						PLCB1_uc010zrb.1_Intron|PLCB1_uc010gbv.1_Intron|PLCB1_uc002wmz.1_Intron|PLCB1_uc002wna.2_Intron	NM_015192	NP_056007			phosphoinositide-specific phospholipase C beta 1						activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12																		---	---	---	---
PLCB1	23236	broad.mit.edu	37	20	8401629	8401629	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8401629delA	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																		---	---	---	---
PLCB4	5332	broad.mit.edu	37	20	9313334	9313334	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9313334delT	uc002wnf.2	+						PLCB4_uc010gbw.1_Intron|PLCB4_uc010gbx.2_Intron|PLCB4_uc002wne.2_Intron	NM_182797	NP_877949			phospholipase C beta 4 isoform b						intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	9945526	9945527	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9945526_9945527insA								PAK7 (125839 upstream) : ANKRD5 (70170 downstream)																																			---	---	---	---
C20orf94	128710	broad.mit.edu	37	20	10438807	10438807	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10438807delT	uc010zre.1	+							NM_001009608	NP_001009608			hypothetical protein LOC128710								protein binding				0																		---	---	---	---
C20orf94	128710	broad.mit.edu	37	20	10537129	10537129	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10537129delT	uc010zre.1	+							NM_001009608	NP_001009608			hypothetical protein LOC128710								protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	11161397	11161398	+	IGR	DEL	TT	-	-	rs5840411		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11161397_11161398delTT								JAG1 (506703 upstream) : BTBD3 (710079 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	11194540	11194541	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11194540_11194541delTT								JAG1 (539846 upstream) : BTBD3 (676936 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	11739692	11739692	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11739692delT								None (None upstream) : BTBD3 (131785 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	11802513	11802513	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11802513delA								None (None upstream) : BTBD3 (68964 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	12597769	12597770	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12597769_12597770delAC								BTBD3 (690527 upstream) : SPTLC3 (391857 downstream)																																			---	---	---	---
SPTLC3	55304	broad.mit.edu	37	20	13003914	13003915	+	Intron	DEL	CA	-	-	rs72221175		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13003914_13003915delCA	uc002wod.1	+						SPTLC3_uc002wob.1_Intron|SPTLC3_uc002woc.2_Intron	NM_018327	NP_060797			serine palmitoyltransferase, long chain base						sphingoid biosynthetic process	integral to membrane|serine C-palmitoyltransferase complex	pyridoxal phosphate binding|serine C-palmitoyltransferase activity|transferase activity, transferring nitrogenous groups				0					Pyridoxal Phosphate(DB00114)													---	---	---	---
TASP1	55617	broad.mit.edu	37	20	13434710	13434712	+	Intron	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13434710_13434712delAAA	uc002woi.2	-						TASP1_uc010zri.1_Intron|TASP1_uc002woh.2_Intron	NM_017714	NP_060184			taspase 1 precursor						asparagine catabolic process via L-aspartate|positive regulation of transcription, DNA-dependent|protein maturation		threonine-type endopeptidase activity				0																		---	---	---	---
ESF1	51575	broad.mit.edu	37	20	13717020	13717020	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13717020delA	uc002woj.2	-							NM_016649	NP_057733			ABT1-associated protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|nucleoplasm				ovary(1)	1																		---	---	---	---
MACROD2	140733	broad.mit.edu	37	20	14178413	14178413	+	Intron	DEL	A	-	-	rs113046439		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14178413delA	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	14529505	14529505	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14529505delA	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	15581429	15581429	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15581429delA	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	15676057	15676057	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15676057delT	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	15795624	15795628	+	Intron	DEL	TTGCA	-	-	rs11469189		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15795624_15795628delTTGCA	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron|MACROD2_uc002wpb.2_Intron	NM_080676	NP_542407			MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	16138788	16138788	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16138788delC								MACROD2 (104949 upstream) : KIF16B (113961 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	17039060	17039060	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17039060delA								OTOR (306252 upstream) : PCSK2 (167692 downstream)																																			---	---	---	---
PCSK2	5126	broad.mit.edu	37	20	17230482	17230482	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17230482delG	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)													---	---	---	---
C20orf72	92667	broad.mit.edu	37	20	17956198	17956198	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17956198delA	uc002wqh.2	+						C20orf72_uc010gco.2_Intron|C20orf72_uc010gcp.2_Intron	NM_052865	NP_443097			hypothetical protein LOC92667												0																		---	---	---	---
DTD1	92675	broad.mit.edu	37	20	18659433	18659433	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18659433delT	uc002wrf.3	+							NM_080820	NP_543010			D-tyrosyl-tRNA deacylase 1						D-amino acid catabolic process	cytoplasm	hydrolase activity, acting on ester bonds			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	19054565	19054565	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19054565delT								C20orf79 (259532 upstream) : SLC24A3 (138725 downstream)																																			---	---	---	---
SLC24A3	57419	broad.mit.edu	37	20	19572138	19572138	+	Intron	DEL	T	-	-	rs67182816		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19572138delT	uc002wrl.2	+							NM_020689	NP_065740			solute carrier family 24							integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(1)	1																		---	---	---	---
SLC24A3	57419	broad.mit.edu	37	20	19609775	19609776	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19609775_19609776delAC	uc002wrl.2	+							NM_020689	NP_065740			solute carrier family 24							integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(1)	1																		---	---	---	---
C20orf26	26074	broad.mit.edu	37	20	20317995	20318002	+	Intron	DEL	TGGGTGGA	-	-	rs111753471		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20317995_20318002delTGGGTGGA	uc002wru.2	+						C20orf26_uc002wrw.2_Intron	NM_015585	NP_056400			hypothetical protein LOC26074											ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)														---	---	---	---
Unknown	0	broad.mit.edu	37	20	21050372	21050372	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21050372delG								RALGAPA2 (357106 upstream) : PLK1S1 (56252 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	21095873	21095873	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21095873delA								RALGAPA2 (402607 upstream) : PLK1S1 (10751 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	21736954	21736955	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21736954_21736955insT								PAX1 (40334 upstream) : LOC284788 (644016 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	21849210	21849210	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21849210delT								PAX1 (152590 upstream) : LOC284788 (531761 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	22284353	22284354	+	IGR	DEL	CT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22284353_22284354delCT								PAX1 (587733 upstream) : LOC284788 (96617 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	22462904	22462904	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22462904delA								LOC284788 (61623 upstream) : C20orf56 (78290 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	23480643	23480644	+	IGR	DEL	GA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23480643_23480644delGA								CST8 (3988 upstream) : CSTT (19139 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	24161517	24161517	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24161517delA								GGTLC1 (192101 upstream) : TMEM90B (288318 downstream)																																			---	---	---	---
ZNF337	26152	broad.mit.edu	37	20	25679551	25679551	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25679551delT	uc002wvb.2	-						ZNF337_uc002wvc.2_5'Flank	NM_015655	NP_056470			zinc finger protein 337						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
FAM182B	728882	broad.mit.edu	37	20	25845928	25845929	+	Intron	DEL	CA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25845928_25845929delCA	uc002wvd.1	-						FAM182B_uc002wve.2_5'Flank					Homo sapiens cDNA FLJ30282 fis, clone BRACE2002803.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	25929808	25929809	+	IGR	INS	-	TT	TT	rs142569238	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25929808_25929809insTT								FAM182B (81022 upstream) : LOC100134868 (60626 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	26132119	26132119	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26132119delT								C20orf191 (37442 upstream) : MIR663 (56703 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	26174457	26174458	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26174457_26174458delTT	uc002wvk.2	-											Homo sapiens hypothetical protein LOC284801, mRNA (cDNA clone IMAGE:4830814).																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	26257926	26257927	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26257926_26257927delTG								MIR663 (69012 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29468322	29468322	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29468322delT								None (None upstream) : FRG1B (143557 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29572296	29572297	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29572296_29572297delAC								None (None upstream) : FRG1B (39582 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29586239	29586239	+	IGR	DEL	T	-	-	rs73620370		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29586239delT								None (None upstream) : FRG1B (25640 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29606467	29606467	+	IGR	DEL	C	-	-	rs112539739		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29606467delC								None (None upstream) : FRG1B (5412 downstream)																																			---	---	---	---
FRG1B	284802	broad.mit.edu	37	20	29613774	29613777	+	Intron	DEL	TACT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29613774_29613777delTACT	uc002wvm.1	+						FRG1B_uc010ztj.1_Intron|FRG1B_uc010gdr.1_Intron|FRG1B_uc010ztk.1_5'Flank	NR_003579				Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0																		---	---	---	---
FRG1B	284802	broad.mit.edu	37	20	29622811	29622812	+	5'Flank	INS	-	T	T	rs112093668		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29622811_29622812insT	uc010ztl.1	+						FRG1B_uc002wvm.1_Intron|FRG1B_uc010ztj.1_Intron|FRG1B_uc010gdr.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0																		---	---	---	---
FRG1B	284802	broad.mit.edu	37	20	29633770	29633771	+	Intron	INS	-	AA	AA	rs145484297	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29633770_29633771insAA	uc010ztl.1	+						FRG1B_uc002wvm.1_Intron|FRG1B_uc010ztj.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0																		---	---	---	---
FRG1B	284802	broad.mit.edu	37	20	29648466	29648467	+	Intron	DEL	TA	-	-	rs140332313		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29648466_29648467delTA	uc010ztl.1	+						FRG1B_uc010ztj.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0																		---	---	---	---
FRG1B	284802	broad.mit.edu	37	20	29648657	29648657	+	Intron	DEL	T	-	-	rs71221959		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29648657delT	uc010ztl.1	+						FRG1B_uc010ztj.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0																		---	---	---	---
FRG1B	284802	broad.mit.edu	37	20	29652356	29652356	+	3'UTR	DEL	T	-	-	rs111401906		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29652356delT	uc010ztl.1	+	4					FRG1B_uc010ztj.1_RNA|FRG1B_uc010ztk.1_3'UTR					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	29811071	29811072	+	IGR	INS	-	GAATGGAATG	GAATGGAATG	rs143004296		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29811071_29811072insGAATGGAATG								FRG1B (157163 upstream) : DEFB115 (34395 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29930733	29930733	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29930733delT								DEFB116 (34345 upstream) : DEFB118 (25695 downstream)																																			---	---	---	---
DEFB122	245935	broad.mit.edu	37	20	30008623	30008624	+	5'Flank	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30008623_30008624insA	uc002wvw.2	+							NR_002577				Homo sapiens defensin, beta 122 (pseudogene) (DEFB122), non-coding RNA.												0																		---	---	---	---
HM13	81502	broad.mit.edu	37	20	30113563	30113563	+	Intron	DEL	A	-	-	rs78847687		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30113563delA	uc002wwe.2	+						HM13_uc002wwc.2_Intron|HM13_uc002wwd.2_Intron|HM13_uc002wwb.1_Intron	NM_030789	NP_110416			minor histocompatibility antigen 13 isoform 1						membrane protein proteolysis	cell surface|endoplasmic reticulum membrane|integral to membrane|plasma membrane	aspartic-type endopeptidase activity|protein binding			breast(1)	1	all_cancers(5;3.44e-05)|Lung NSC(7;4.38e-06)|all_lung(7;7.65e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		all cancers(5;0.000479)|Colorectal(19;0.00202)|COAD - Colon adenocarcinoma(19;0.0264)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	30188800	30188800	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30188800delA								HM13 (31432 upstream) : ID1 (4292 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	30213464	30213465	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30213464_30213465delAA								ID1 (19151 upstream) : COX4I2 (12226 downstream)																																			---	---	---	---
TTLL9	164395	broad.mit.edu	37	20	30484345	30484345	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30484345delT	uc010gdx.1	+						TTLL9_uc002wwy.1_Intron|TTLL9_uc002wwz.1_Intron|TTLL9_uc002wxa.1_Intron|TTLL9_uc002wxb.1_Intron|TTLL9_uc010zto.1_Intron|TTLL9_uc002wxc.2_Intron|TTLL9_uc010ztp.1_Intron	NM_001008409	NP_001008409			tubulin tyrosine ligase-like family, member 9						protein modification process	cilium|microtubule|microtubule basal body	ATP binding|tubulin-tyrosine ligase activity			ovary(2)	2			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)															---	---	---	---
TM9SF4	9777	broad.mit.edu	37	20	30704634	30704635	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30704634_30704635delTT	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	31181418	31181418	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31181418delG	uc002wxy.2	+											RecName: Full=Putative uncharacterized protein MGC163334;																														---	---	---	---
DNMT3B	1789	broad.mit.edu	37	20	31366171	31366172	+	Intron	DEL	AA	-	-	rs33960116		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31366171_31366172delAA	uc002wyc.2	+						DNMT3B_uc010ztx.1_Intron|DNMT3B_uc010zty.1_Intron|DNMT3B_uc002wyd.2_Intron|DNMT3B_uc002wye.2_Intron|DNMT3B_uc010gee.2_Intron|DNMT3B_uc010gef.2_Intron|DNMT3B_uc010ztz.1_Intron|DNMT3B_uc010zua.1_Intron|DNMT3B_uc002wyf.2_5'Flank	NM_006892	NP_008823			DNA cytosine-5 methyltransferase 3 beta isoform						negative regulation of histone H3-K9 methylation|positive regulation of gene expression|positive regulation of histone H3-K4 methylation		metal ion binding|protein binding|transcription corepressor activity			lung(3)|ovary(2)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	31801949	31801949	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31801949delT								BASE (3681 upstream) : C20orf71 (3186 downstream)																																			---	---	---	---
CBFA2T2	9139	broad.mit.edu	37	20	32146432	32146432	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32146432delT	uc002wze.1	+						CBFA2T2_uc010zug.1_Intron	NM_001032999	NP_001028171			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	32470698	32470698	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32470698delA								CHMP4B (28529 upstream) : RALY (111034 downstream)																																			---	---	---	---
RALY	22913	broad.mit.edu	37	20	32600248	32600249	+	Intron	INS	-	CTCTTCTCTTT	CTCTTCTCTTT	rs138654658	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32600248_32600249insCTCTTCTCTTT	uc002xab.2	+						RALY_uc010zui.1_Intron|RALY_uc002xac.2_Intron|RALY_uc002xad.2_Intron|RALY_uc002xae.1_Intron	NM_016732	NP_057951			RNA binding protein (autoantigenic,							catalytic step 2 spliceosome|heterogeneous nuclear ribonucleoprotein complex	nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
DYNLRB1	83658	broad.mit.edu	37	20	33108832	33108832	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33108832delT	uc002xal.2	+						DYNLRB1_uc010zuk.1_Intron|DYNLRB1_uc002xam.2_Intron|DYNLRB1_uc002xan.2_Intron	NM_014183	NP_054902			Roadblock-1						microtubule-based movement|transport|visual behavior	centrosome|cytoplasmic dynein complex|microtubule	microtubule motor activity				0																		---	---	---	---
GDF5	8200	broad.mit.edu	37	20	33971656	33971656	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33971656delA	uc010gfc.1	-						UQCC_uc010zuy.1_Intron|UQCC_uc002xcd.2_Intron|UQCC_uc010zuz.1_Intron|UQCC_uc010zva.1_Intron|UQCC_uc002xce.2_Intron|UQCC_uc002xcg.2_Intron|UQCC_uc010gfb.2_Intron|UQCC_uc010zvb.1_Intron|UQCC_uc002xcf.2_Intron|UQCC_uc002xci.1_Intron|UQCC_uc010gfd.1_Intron	NM_000557	NP_000548			growth differentiation factor 5 preproprotein						cartilage development|cell-cell signaling|growth|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity				0	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)															---	---	---	---
CEP250	11190	broad.mit.edu	37	20	34080977	34080977	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34080977delT	uc002xcm.2	+						CEP250_uc010zve.1_Intron	NM_007186	NP_009117			centrosomal protein 2						centriole-centriole cohesion|G2/M transition of mitotic cell cycle|protein localization|regulation of centriole-centriole cohesion	centriole|cilium|cytosol|microtubule basal body|perinuclear region of cytoplasm|protein complex	protein C-terminus binding|protein kinase binding			ovary(4)|central_nervous_system(1)	5	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)															---	---	---	---
CEP250	11190	broad.mit.edu	37	20	34096147	34096148	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34096147_34096148delTT	uc002xcm.2	+						CEP250_uc010zve.1_Intron	NM_007186	NP_009117			centrosomal protein 2						centriole-centriole cohesion|G2/M transition of mitotic cell cycle|protein localization|regulation of centriole-centriole cohesion	centriole|cilium|cytosol|microtubule basal body|perinuclear region of cytoplasm|protein complex	protein C-terminus binding|protein kinase binding			ovary(4)|central_nervous_system(1)	5	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)															---	---	---	---
RBM39	9584	broad.mit.edu	37	20	34292683	34292683	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34292683delA	uc002xeb.2	-						RBM39_uc002xdz.2_Intron|RBM39_uc002xea.2_Intron|RBM39_uc010gfn.2_Intron|RBM39_uc010zvm.1_Intron|RBM39_uc002xeg.2_Intron|RBM39_uc002xec.2_Intron|RBM39_uc002xed.2_Intron|RBM39_uc002xee.2_Intron|RBM39_uc002xef.2_Intron|RBM39_uc010zvn.1_Intron	NM_184234	NP_909122			RNA binding motif protein 39 isoform a						mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|transcription, DNA-dependent	centrosome|nuclear speck	nucleotide binding|protein binding|RNA binding			ovary(1)|central_nervous_system(1)	2	all_epithelial(2;0.00295)|Lung NSC(9;0.00453)|Breast(12;0.00544)|all_lung(11;0.00676)																	---	---	---	---
C20orf152	140894	broad.mit.edu	37	20	34554572	34554572	+	5'Flank	DEL	T	-	-	rs113244350		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34554572delT	uc002xes.1	+						C20orf152_uc002xer.1_5'Flank|C20orf152_uc010gfp.1_5'Flank					SubName: Full=C20orf152 protein;												0	Breast(12;0.00631)																	---	---	---	---
EPB41L1	2036	broad.mit.edu	37	20	34726805	34726805	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34726805delT	uc002xev.2	+						EPB41L1_uc002xeu.2_Intron|EPB41L1_uc010zvo.1_Intron|EPB41L1_uc002xew.2_Intron|EPB41L1_uc002xex.2_Intron|EPB41L1_uc002xey.2_Intron|EPB41L1_uc002xez.2_Intron	NM_012156	NP_036288			erythrocyte membrane protein band 4.1-like 1						cortical actin cytoskeleton organization|synaptic transmission	cytoskeleton|cytosol|extrinsic to membrane|plasma membrane	actin binding|structural molecule activity			ovary(2)|pancreas(1)	3	Breast(12;0.0239)															OREG0025898	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
EPB41L1	2036	broad.mit.edu	37	20	34762191	34762191	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34762191delT	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)																	---	---	---	---
EPB41L1	2036	broad.mit.edu	37	20	34765606	34765606	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34765606delC	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)																	---	---	---	---
DLGAP4	22839	broad.mit.edu	37	20	35024907	35024908	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35024907_35024908delAC	uc002xff.2	+						DLGAP4_uc010zvp.1_Intron	NM_014902	NP_055717			disks large-associated protein 4 isoform a						cell-cell signaling	membrane	protein binding			skin(2)|ovary(1)	3	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)																---	---	---	---
DLGAP4	22839	broad.mit.edu	37	20	35149115	35149115	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35149115delT	uc002xff.2	+						DLGAP4_uc010zvp.1_Intron|DLGAP4_uc002xfg.2_Intron|DLGAP4_uc002xfh.2_Intron|DLGAP4_uc002xfi.2_Intron|DLGAP4_uc002xfj.2_Intron|uc002xfk.3_Intron	NM_014902	NP_055717			disks large-associated protein 4 isoform a						cell-cell signaling	membrane	protein binding			skin(2)|ovary(1)	3	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)																---	---	---	---
TGIF2	60436	broad.mit.edu	37	20	35209530	35209531	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35209530_35209531insA	uc002xfn.2	+						C20orf24_uc002xfo.2_Intron	NM_021809	NP_068581			TGFB-induced factor homeobox 2							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			pancreas(1)|skin(1)	2	Breast(12;0.114)	Myeloproliferative disorder(115;0.00878)																---	---	---	---
C20orf24	55969	broad.mit.edu	37	20	35239841	35239841	+	Intron	DEL	A	-	-	rs80108840		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35239841delA	uc002xfq.2	+						C20orf24_uc002xfo.2_Intron|C20orf24_uc002xfp.2_Intron|C20orf24_uc002xft.2_Intron|C20orf24_uc002xfr.2_Intron|C20orf24_uc002xfs.2_Intron	NM_018840	NP_061328			RAB5-interacting protein isoform a								protein binding				0	Breast(12;0.114)	Myeloproliferative disorder(115;0.00878)																---	---	---	---
C20orf117	140710	broad.mit.edu	37	20	35465548	35465548	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35465548delC	uc002xgd.1	-							NM_199181	NP_954650			hypothetical protein LOC140710 isoform 2												0		Myeloproliferative disorder(115;0.00874)																---	---	---	---
C20orf132	140699	broad.mit.edu	37	20	35745383	35745384	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35745383_35745384delTT	uc010zvu.1	-						C20orf132_uc002xgk.2_Intron	NM_152503	NP_689716			hypothetical protein LOC140699 isoform 1												0		Myeloproliferative disorder(115;0.00878)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	36102089	36102089	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36102089delT								SRC (68270 upstream) : BLCAP (43731 downstream)																																			---	---	---	---
RPRD1B	58490	broad.mit.edu	37	20	36676670	36676670	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36676670delT	uc002xho.3	+							NM_021215	NP_067038			Regulation of nuclear pre-mRNA domain containing											pancreas(1)	1																		---	---	---	---
RALGAPB	57148	broad.mit.edu	37	20	37175230	37175230	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37175230delA	uc002xiw.2	+						RALGAPB_uc002xix.2_Intron|RALGAPB_uc002xiy.1_Intron|RALGAPB_uc002xiz.2_Intron|RALGAPB_uc002xja.1_3'UTR	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	37995718	37995718	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37995718delG								LOC339568 (142327 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	38252242	38252242	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:38252242delA								LOC339568 (398851 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	39170132	39170133	+	IGR	INS	-	T	T	rs112348083		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39170132_39170133insT								None (None upstream) : MAFB (144386 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	39575990	39575990	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39575990delA								MAFB (258114 upstream) : TOP1 (81472 downstream)																																			---	---	---	---
TOP1	7150	broad.mit.edu	37	20	39708709	39708709	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39708709delT	uc002xjl.2	+						TOP1_uc010gge.1_Intron	NM_003286	NP_003277			DNA topoisomerase I						DNA topological change|interspecies interaction between organisms|phosphorylation|programmed cell death|response to drug	chromosome|nucleolus|nucleoplasm	ATP binding|chromatin DNA binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA topoisomerase type I activity|protein binding			breast(3)|ovary(2)|central_nervous_system(1)|kidney(1)	7		Myeloproliferative disorder(115;0.00878)			Irinotecan(DB00762)|Lucanthone(DB04967)|Topotecan(DB01030)			T	NUP98	AML*								---	---	---	---
ZHX3	23051	broad.mit.edu	37	20	39906989	39906989	+	Intron	DEL	A	-	-	rs77376869		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39906989delA	uc002xjs.1	-						ZHX3_uc002xjt.1_Intron|ZHX3_uc002xju.1_Intron|ZHX3_uc002xjv.1_Intron|ZHX3_uc002xjw.1_Intron	NM_015035	NP_055850			zinc fingers and homeoboxes 3						negative regulation of transcription, DNA-dependent	cytoplasm|nucleolus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3		Myeloproliferative disorder(115;0.00425)																---	---	---	---
CHD6	84181	broad.mit.edu	37	20	40120107	40120108	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40120107_40120108delAA	uc002xka.1	-						CHD6_uc002xkd.2_Intron	NM_032221	NP_115597			chromodomain helicase DNA binding protein 6						chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|skin(5)|lung(2)|central_nervous_system(1)	14		Myeloproliferative disorder(115;0.00425)																---	---	---	---
PTPRT	11122	broad.mit.edu	37	20	41415252	41415252	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41415252delC	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	41447082	41447082	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41447082delA	uc002xkg.2	-						PTPRT_uc010ggj.2_Intron	NM_007050	NP_008981			protein tyrosine phosphatase, receptor type, T						homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	41859347	41859347	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41859347delA								PTPRT (40790 upstream) : SFRS6 (227157 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	41899706	41899706	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41899706delA								PTPRT (81149 upstream) : SFRS6 (186798 downstream)																																			---	---	---	---
IFT52	51098	broad.mit.edu	37	20	42226012	42226014	+	Intron	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42226012_42226014delAAA	uc002xkw.2	+						IFT52_uc010zwi.1_Intron|IFT52_uc002xky.2_Intron|IFT52_uc002xkx.2_Intron|IFT52_uc010ggn.2_Intron|IFT52_uc002xkz.2_Intron	NM_016004	NP_057088			intraflagellar transport 52 homolog							intraflagellar transport particle B|microtubule-based flagellum	protein C-terminus binding			ovary(2)	2		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)															---	---	---	---
MYBL2	4605	broad.mit.edu	37	20	42318833	42318833	+	Intron	DEL	T	-	-	rs113608338		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42318833delT	uc002xlb.1	+						MYBL2_uc010zwj.1_Intron|MYBL2_uc002xla.1_Intron	NM_002466	NP_002457			MYB-related protein B							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			lung(3)|kidney(2)	5		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)															---	---	---	---
MYBL2	4605	broad.mit.edu	37	20	42342032	42342032	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42342032delT	uc002xlb.1	+						MYBL2_uc010zwj.1_Intron	NM_002466	NP_002457			MYB-related protein B							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			lung(3)|kidney(2)	5		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)															---	---	---	---
JPH2	57158	broad.mit.edu	37	20	42780157	42780157	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42780157delA	uc002xli.1	-							NM_020433	NP_065166			junctophilin 2 isoform 1						calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane|plasma membrane					0		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	42859009	42859009	+	IGR	DEL	A	-	-	rs77785005		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42859009delA								C20orf111 (19578 upstream) : GDAP1L1 (16899 downstream)																																			---	---	---	---
PKIG	11142	broad.mit.edu	37	20	43229333	43229333	+	Intron	DEL	A	-	-	rs74367824		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43229333delA	uc002xmg.2	+						PKIG_uc002xmh.2_Intron|PKIG_uc002xmi.2_Intron	NM_181805	NP_861521			cAMP-dependent protein kinase inhibitor gamma								cAMP-dependent protein kinase inhibitor activity|protein binding				0		Myeloproliferative disorder(115;0.0122)	Colorectal(3;0.001)|COAD - Colon adenocarcinoma(18;0.00189)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	44119407	44119407	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44119407delA								WFDC2 (9236 upstream) : SPINT3 (21694 downstream)																																			---	---	---	---
WFDC8	90199	broad.mit.edu	37	20	44184633	44184633	+	Intron	DEL	A	-	-	rs78363134		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44184633delA	uc002xow.2	-						WFDC8_uc002xox.2_Intron	NM_181510	NP_852611			WAP four-disulfide core domain 8 precursor							extracellular region	serine-type endopeptidase inhibitor activity				0		Myeloproliferative disorder(115;0.0122)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	45105982	45105982	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45105982delT								LOC100240726 (12051 upstream) : ZNF334 (23727 downstream)																																			---	---	---	---
EYA2	2139	broad.mit.edu	37	20	45525044	45525045	+	Intron	DEL	AA	-	-	rs71892947		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45525044_45525045delAA	uc002xsm.2	+						EYA2_uc010ghp.2_Intron	NM_005244	NP_005235			eyes absent 2 isoform a						DNA repair|histone dephosphorylation|mesodermal cell fate specification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	magnesium ion binding|protein binding|protein tyrosine phosphatase activity			ovary(1)	1		Myeloproliferative disorder(115;0.0241)																---	---	---	---
ZMYND8	23613	broad.mit.edu	37	20	45976870	45976870	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45976870delT	uc002xta.1	-						ZMYND8_uc010ghr.1_5'Flank|ZMYND8_uc002xst.1_5'Flank|ZMYND8_uc002xsu.1_5'Flank|ZMYND8_uc002xsv.1_5'Flank|ZMYND8_uc002xsw.1_5'Flank|ZMYND8_uc002xsx.1_5'Flank|ZMYND8_uc002xsy.1_5'Flank|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_5'Flank|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	46044806	46044816	+	IGR	DEL	AGGAAGGAGGA	-	-	rs145610421		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46044806_46044816delAGGAAGGAGGA								ZMYND8 (59332 upstream) : NCOA3 (85841 downstream)																																			---	---	---	---
CSE1L	1434	broad.mit.edu	37	20	47704469	47704469	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47704469delT	uc002xty.2	+						CSE1L_uc010zyg.1_Intron|CSE1L_uc010ghx.2_Intron|CSE1L_uc010ghy.2_Intron|CSE1L_uc010zyh.1_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	48871520	48871520	+	IGR	DEL	T	-	-	rs71337319		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48871520delT								CEBPB (62308 upstream) : PTPN1 (255371 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	49068651	49068651	+	IGR	DEL	A	-	-	rs71190560		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49068651delA								CEBPB (259439 upstream) : PTPN1 (58240 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	49071632	49071633	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49071632_49071633delTC								CEBPB (262420 upstream) : PTPN1 (55258 downstream)																																			---	---	---	---
KCNG1	3755	broad.mit.edu	37	20	49623091	49623091	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49623091delT	uc002xwa.3	-							NM_002237	NP_002228			potassium voltage-gated channel, subfamily G,							voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	49652046	49652046	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49652046delA								KCNG1 (12371 upstream) : NFATC2 (355720 downstream)																																			---	---	---	---
NFATC2	4773	broad.mit.edu	37	20	50046454	50046454	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50046454delC	uc002xwd.2	-						NFATC2_uc002xwc.2_Intron|NFATC2_uc010zyv.1_Intron|NFATC2_uc010zyw.1_Intron|NFATC2_uc010zyx.1_Intron|NFATC2_uc010zyy.1_Intron|NFATC2_uc010zyz.1_Intron|NFATC2_uc002xwe.2_Intron	NM_173091	NP_775114			nuclear factor of activated T-cells,						B cell receptor signaling pathway|positive regulation of B cell proliferation|response to DNA damage stimulus|response to drug	actin cytoskeleton|nucleus|plasma membrane	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2	Hepatocellular(150;0.248)																	---	---	---	---
ATP9A	10079	broad.mit.edu	37	20	50250463	50250464	+	Intron	DEL	GA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50250463_50250464delGA	uc002xwg.1	-						ATP9A_uc010gih.1_Intron|ATP9A_uc002xwf.1_Intron	NM_006045	NP_006036			ATPase, class II, type 9A						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(4)	4																		---	---	---	---
ATP9A	10079	broad.mit.edu	37	20	50286409	50286409	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50286409delA	uc002xwg.1	-						ATP9A_uc010gih.1_Intron|ATP9A_uc002xwf.1_Intron	NM_006045	NP_006036			ATPase, class II, type 9A						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	51049233	51049235	+	IGR	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51049233_51049235delTTT								ZFP64 (240709 upstream) : TSHZ2 (539642 downstream)																																			---	---	---	---
TSHZ2	128553	broad.mit.edu	37	20	52042341	52042342	+	Intron	DEL	TT	-	-	rs11476894		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52042341_52042342delTT	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)															---	---	---	---
ZNF217	7764	broad.mit.edu	37	20	52195614	52195614	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52195614delG	uc002xwq.3	-						ZNF217_uc010gij.1_Intron	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	52283297	52283298	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52283297_52283298delTT								ZNF217 (72496 upstream) : SUMO1P1 (207744 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	52489299	52489300	+	IGR	DEL	GT	-	-	rs149182050		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52489299_52489300delGT								ZNF217 (278498 upstream) : SUMO1P1 (1742 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	52895813	52895813	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52895813delT								PFDN4 (59322 upstream) : DOK5 (196444 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	53773856	53773856	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53773856delT								DOK5 (506147 upstream) : CBLN4 (798641 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54153044	54153045	+	IGR	DEL	GA	-	-	rs11471124		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54153044_54153045delGA								DOK5 (885335 upstream) : CBLN4 (419452 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54568751	54568752	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54568751_54568752delAA								None (None upstream) : CBLN4 (3745 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	55693920	55693920	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55693920delA								TFAP2C (479584 upstream) : BMP7 (49889 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	56329969	56329969	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56329969delT								PMEPA1 (43428 upstream) : C20orf85 (396014 downstream)																																			---	---	---	---
RAB22A	57403	broad.mit.edu	37	20	56901203	56901203	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56901203delT	uc002xyz.2	+							NM_020673	NP_065724			RAS-related protein RAB-22A						endocytosis|endosome organization|protein transport|small GTPase mediated signal transduction	early endosome|endosome membrane|plasma membrane	GTP binding|GTPase activity|protein binding				0	all_epithelial(3;5.09e-14)|Lung NSC(12;0.000122)|all_lung(29;0.00042)		BRCA - Breast invasive adenocarcinoma(13;6.2e-12)|Epithelial(14;4.73e-08)|all cancers(14;4.83e-07)															---	---	---	---
GNAS	2778	broad.mit.edu	37	20	57447591	57447591	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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)			---	---	---	---
Unknown	0	broad.mit.edu	37	20	57589570	57589571	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57589570_57589571insA								CTSZ (7261 upstream) : TUBB1 (4738 downstream)																																			---	---	---	---
PHACTR3	116154	broad.mit.edu	37	20	58349814	58349814	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58349814delA	uc002yau.2	+						PHACTR3_uc002yat.2_Intron|PHACTR3_uc010zzw.1_Intron|PHACTR3_uc002yav.2_Intron|PHACTR3_uc002yaw.2_Intron|PHACTR3_uc002yax.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	58426598	58426598	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58426598delT								PHACTR3 (3834 upstream) : SYCP2 (12021 downstream)																																			---	---	---	---
SYCP2	10388	broad.mit.edu	37	20	58443050	58443051	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58443050_58443051insT	uc002yaz.2	-							NM_014258	NP_055073			synaptonemal complex protein 2						cell division|meiotic prophase I|synaptonemal complex assembly		DNA binding			ovary(3)|lung(2)	5	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)															---	---	---	---
C20orf197	284756	broad.mit.edu	37	20	58636807	58636808	+	Intron	DEL	CA	-	-	rs140756189		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58636807_58636808delCA	uc002ybj.1	+							NM_173644	NP_775915			hypothetical protein LOC284756											upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3			BRCA - Breast invasive adenocarcinoma(7;2.33e-09)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	58687881	58687882	+	IGR	INS	-	T	T	rs144516406	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58687881_58687882insT								C20orf197 (39873 upstream) : MIR646 (195650 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	59180923	59180923	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59180923delT	uc010gjw.1	+											Homo sapiens cDNA FLJ35486 fis, clone SMINT2008491.																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	59339298	59339299	+	IGR	INS	-	ACACACAC	ACACACAC			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59339298_59339299insACACACAC								MIR646 (455673 upstream) : CDH4 (488260 downstream)																																			---	---	---	---
CDH4	1002	broad.mit.edu	37	20	59925770	59925771	+	Intron	DEL	CC	-	-	rs10534860		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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)															---	---	---	---
C20orf166	128826	broad.mit.edu	37	20	61166403	61166404	+	Intron	INS	-	GT	GT	rs139948204	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61166403_61166404insGT	uc011aaj.1	+							NM_178463	NP_848558			hypothetical protein LOC128826												0	Breast(26;1.04e-08)		BRCA - Breast invasive adenocarcinoma(19;7.17e-06)															---	---	---	---
DIDO1	11083	broad.mit.edu	37	20	61513511	61513511	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61513511delG	uc002ydr.1	-	16	4061	c.3797delC	c.(3796-3798)CCTfs	p.P1266fs	DIDO1_uc002yds.1_Frame_Shift_Del_p.P1266fs	NM_033081	NP_149072	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1 isoform c	1266	Pro-rich.				apoptosis|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(3)|skin(3)	6	Breast(26;5.68e-08)																	---	---	---	---
Unknown	0	broad.mit.edu	37	20	61852867	61852875	+	IGR	DEL	TGCAGGGAT	-	-	rs113658090	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61852867_61852875delTGCAGGGAT								YTHDF1 (5329 upstream) : BIRC7 (14401 downstream)																																			---	---	---	---
NKAIN4	128414	broad.mit.edu	37	20	61874139	61874139	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61874139delG	uc002yek.2	-							NM_152864	NP_690603			Na+/K+ transporting ATPase interacting 4							integral to membrane|plasma membrane					0	all_cancers(38;2.72e-09)																	---	---	---	---
CHRNA4	1137	broad.mit.edu	37	20	61988461	61988461	+	Intron	DEL	T	-	-	rs57831004		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61988461delT	uc002yes.2	-						CHRNA4_uc002yet.1_Intron|CHRNA4_uc011aaw.1_Intron|CHRNA4_uc010gke.1_Intron|CHRNA4_uc002yev.1_Intron|CHRNA4_uc010gkf.1_Intron	NM_000744	NP_000735			cholinergic receptor, nicotinic, alpha 4 subunit						B cell activation|behavioral response to nicotine|calcium ion transport|cognition|DNA repair|membrane depolarization|regulation of action potential|regulation of dopamine secretion|regulation of inhibitory postsynaptic membrane potential|response to hypoxia|response to oxidative stress|sensory perception of pain|synaptic transmission, cholinergic	cell junction|dendrite|external side of plasma membrane|membrane fraction|neuronal cell body|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity			central_nervous_system(1)|skin(1)	2	all_cancers(38;1.71e-10)				Nicotine(DB00184)|Varenicline(DB01273)													---	---	---	---
PTK6	5753	broad.mit.edu	37	20	62161846	62161846	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62161846delC	uc002yfg.2	-						PTK6_uc011aay.1_Intron|PTK6_uc011aaz.1_Intron	NM_005975	NP_005966			PTK6 protein tyrosine kinase 6							cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			stomach(1)|kidney(1)	2	all_cancers(38;2.51e-11)		Epithelial(9;1.5e-08)|all cancers(9;8.67e-08)|BRCA - Breast invasive adenocarcinoma(10;6.43e-06)															---	---	---	---
PRPF6	24148	broad.mit.edu	37	20	62648293	62648295	+	Intron	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62648293_62648295delTTT	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)																	---	---	---	---
PRPF6	24148	broad.mit.edu	37	20	62651767	62651767	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62651767delT	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)																	---	---	---	---
PRPF6	24148	broad.mit.edu	37	20	62651768	62651769	+	Intron	INS	-	A	A	rs112671661		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62651768_62651769insA	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)																	---	---	---	---
PRPF6	24148	broad.mit.edu	37	20	62653257	62653258	+	Intron	INS	-	CA	CA			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62653257_62653258insCA	uc002yho.2	+						PRPF6_uc002yhp.2_Intron	NM_012469	NP_036601			PRP6 pre-mRNA processing factor 6 homolog						assembly of spliceosomal tri-snRNP|positive regulation of transcription from RNA polymerase II promoter|spliceosome assembly	catalytic step 2 spliceosome|nucleoplasm|U4/U6 snRNP|U4/U6 x U5 tri-snRNP complex|U5 snRNP	androgen receptor binding|ribonucleoprotein binding|transcription coactivator activity			ovary(2)	2	all_cancers(38;6.47e-12)|all_epithelial(29;1.26e-13)|Lung NSC(23;9.37e-10)|all_lung(23;3.23e-09)																	---	---	---	---
Unknown	0	broad.mit.edu	37	21	9843312	9843313	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9843312_9843313delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	9849619	9849622	+	IGR	DEL	AATT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9849619_9849622delAATT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	9851113	9851113	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9851113delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10432231	10432231	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10432231delA								None (None upstream) : TPTE (474512 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10561146	10561146	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10561146delA	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	10601010	10601010	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10601010delA								None (None upstream) : TPTE (305733 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10811684	10811685	+	IGR	INS	-	GTGGA	GTGGA	rs140720340		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10811684_10811685insGTGGA								None (None upstream) : TPTE (95058 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10843980	10843987	+	IGR	DEL	AATAAAAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10843980_10843987delAATAAAAA								None (None upstream) : TPTE (62756 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10892172	10892172	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10892172delT								None (None upstream) : TPTE (14571 downstream)																																			---	---	---	---
TPTE	7179	broad.mit.edu	37	21	10939548	10939548	+	Intron	DEL	T	-	-	rs113663078		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10939548delT	uc002yip.1	-						TPTE_uc002yis.1_Intron|TPTE_uc002yiq.1_Intron|TPTE_uc002yir.1_Intron|TPTE_uc010gkv.1_Intron	NM_199261	NP_954870			transmembrane phosphatase with tensin homology						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)														---	---	---	---
TPTE	7179	broad.mit.edu	37	21	10954709	10954709	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10954709delA	uc002yip.1	-						TPTE_uc002yis.1_Intron|TPTE_uc002yiq.1_Intron|TPTE_uc002yir.1_Intron|TPTE_uc010gkv.1_Intron	NM_199261	NP_954870			transmembrane phosphatase with tensin homology						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)														---	---	---	---
BAGE2	85319	broad.mit.edu	37	21	11050605	11050606	+	Intron	INS	-	A	A	rs150695624		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11050605_11050606insA	uc002yit.1	-							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)														---	---	---	---
BAGE2	85319	broad.mit.edu	37	21	11075686	11075687	+	Intron	INS	-	TGA	TGA	rs4009958		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11075686_11075687insTGA	uc002yit.1	-						BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	11144771	11144772	+	IGR	DEL	TC	-	-	rs55756166		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11144771_11144772delTC								BAGE (45834 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	14750463	14750463	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14750463delT								C21orf99 (259894 upstream) : POTED (232035 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	14816664	14816665	+	IGR	DEL	AC	-	-	rs469452	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14816664_14816665delAC								C21orf99 (326095 upstream) : POTED (165833 downstream)																																			---	---	---	---
RBM11	54033	broad.mit.edu	37	21	15587131	15587131	+	5'Flank	DEL	A	-	-	rs67384588		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15587131delA	uc002yjo.3	+						RBM11_uc002yjn.3_5'Flank|RBM11_uc002yjp.3_5'Flank	NM_144770	NP_658983			RNA binding motif protein 11								nucleotide binding|RNA binding				0				Epithelial(23;0.000314)|COAD - Colon adenocarcinoma(22;0.00242)|Colorectal(24;0.0129)|Lung(58;0.141)														---	---	---	---
SAMSN1	64092	broad.mit.edu	37	21	15882998	15882999	+	Intron	INS	-	CT	CT	rs148834350	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15882998_15882999insCT	uc002yju.1	-						SAMSN1_uc010gky.1_Intron|SAMSN1_uc002yjv.1_Intron	NM_022136	NP_071419			SAM domain, SH3 domain and nuclear localization						negative regulation of adaptive immune response|negative regulation of B cell activation|negative regulation of peptidyl-tyrosine phosphorylation	cytoplasm|nucleus|ruffle	phosphotyrosine binding			ovary(3)|pancreas(1)	4				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.00118)|Colorectal(24;0.00961)|Lung(58;0.164)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	16767756	16767756	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16767756delA								NRIP1 (330630 upstream) : USP25 (334740 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	16854871	16854871	+	IGR	DEL	T	-	-	rs9981812	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16854871delT								NRIP1 (417745 upstream) : USP25 (247625 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	16899056	16899056	+	IGR	DEL	A	-	-	rs67166113		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16899056delA								NRIP1 (461930 upstream) : USP25 (203440 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	18572297	18572298	+	IGR	DEL	AC	-	-	rs34365786		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18572297_18572298delAC								C21orf34 (590203 upstream) : CXADR (313032 downstream)																																			---	---	---	---
CXADR	1525	broad.mit.edu	37	21	18931674	18931675	+	Intron	DEL	TA	-	-	rs144252955	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18931674_18931675delTA	uc002yki.2	+						CXADR_uc002ykh.1_Intron|CXADR_uc010gld.1_Intron|CXADR_uc010gle.1_Intron|CXADR_uc002ykj.1_Intron	NM_001338	NP_001329			coxsackie virus and adenovirus receptor						blood coagulation|cell adhesion|interspecies interaction between organisms|leukocyte migration|regulation of immune response	adherens junction|basolateral plasma membrane|extracellular region|integral to plasma membrane|nucleus|tight junction	receptor activity			ovary(1)	1				Epithelial(23;0.000206)|all cancers(11;0.000302)|OV - Ovarian serous cystadenocarcinoma(11;0.0194)|Lung(58;0.0233)|COAD - Colon adenocarcinoma(22;0.0389)|Colorectal(24;0.0483)|LUSC - Lung squamous cell carcinoma(23;0.0782)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	19027056	19027056	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19027056delG								BTG3 (41788 upstream) : C21orf91 (122667 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	19078840	19078841	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19078840_19078841insT								BTG3 (93572 upstream) : C21orf91 (70882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	19784332	19784332	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19784332delA								TMPRSS15 (8362 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	20385500	20385502	+	IGR	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20385500_20385502delAAA								TMPRSS15 (609530 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	20541521	20541522	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20541521_20541522delTT								TMPRSS15 (765551 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	21797194	21797194	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:21797194delT								None (None upstream) : C21orf131 (317720 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	23121128	23121128	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:23121128delG	uc002yle.2	+											Homo sapiens, clone IMAGE:5547749, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	24099917	24099918	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:24099917_24099918delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	25546574	25546575	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:25546574_25546575insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	26009504	26009504	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26009504delA								None (None upstream) : NCRNA00158 (748630 downstream)																																			---	---	---	---
GABPA	2551	broad.mit.edu	37	21	27134768	27134768	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27134768delT	uc002ylx.3	+						GABPA_uc002yly.3_Intron	NM_002040	NP_002031			GA binding protein transcription factor, alpha						positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	protein heterodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription regulatory region DNA binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
APP	351	broad.mit.edu	37	21	27382268	27382268	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27382268delA	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)																---	---	---	---
APP	351	broad.mit.edu	37	21	27457447	27457447	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27457447delT	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)																---	---	---	---
ADAMTS1	9510	broad.mit.edu	37	21	28219511	28219511	+	5'Flank	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28219511delC	uc002ymf.2	-							NM_006988	NP_008919			ADAM metallopeptidase with thrombospondin type 1						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	28912771	28912771	+	IGR	DEL	A	-	-	rs113712817		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28912771delA								ADAMTS5 (573332 upstream) : NCRNA00113 (181927 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	29424065	29424065	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:29424065delA	uc002ymk.1	+											Homo sapiens cDNA FLJ35800 fis, clone TESTI2005933.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	29996303	29996303	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:29996303delA								NCRNA00161 (83627 upstream) : N6AMT1 (248210 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	30121872	30121872	+	IGR	DEL	C	-	-	rs138806279		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30121872delC								NCRNA00161 (209196 upstream) : N6AMT1 (122641 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	30280467	30280468	+	IGR	INS	-	CTTGTTGTT	CTTGTTGTT	rs58436729	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30280467_30280468insCTTGTTGTT								N6AMT1 (22774 upstream) : RNF160 (19998 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	30369867	30369867	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30369867delG								RNF160 (4590 upstream) : RWDD2B (8215 downstream)																																			---	---	---	---
C21orf7	56911	broad.mit.edu	37	21	30483594	30483596	+	Intron	DEL	AAC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30483594_30483596delAAC	uc002yne.2	+						C21orf7_uc011acr.1_Intron|C21orf7_uc002ynd.2_Intron|C21orf7_uc010gln.2_Intron|C21orf7_uc002ynf.2_Intron	NM_020152	NP_064537			chromosome 21 open reading frame 7							cytosol|nucleus	protein binding			ovary(2)	2				Colorectal(56;0.248)														---	---	---	---
NCRNA00189	193629	broad.mit.edu	37	21	30601256	30601256	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30601256delT	uc002ynh.2	+						NCRNA00189_uc002yni.2_Intron	NR_027072				Homo sapiens chromosome 21 open reading frame 109 (C21orf109) mRNA, complete cds.												0																		---	---	---	---
GRIK1	2897	broad.mit.edu	37	21	31169452	31169452	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31169452delA	uc002yno.1	-						GRIK1_uc002ynn.2_Intron|GRIK1_uc011acs.1_Intron|GRIK1_uc011act.1_Intron|GRIK1_uc010glq.1_Intron|GRIK1_uc002ynr.2_Intron	NM_000830	NP_000821			glutamate receptor, ionotropic, kainate 1						central nervous system development|synaptic transmission	cell junction|postsynaptic membrane	kainate selective glutamate receptor activity			large_intestine(1)|ovary(1)|skin(1)	3					L-Glutamic Acid(DB00142)|Topiramate(DB00273)													---	---	---	---
TIAM1	7074	broad.mit.edu	37	21	32600232	32600232	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32600232delT	uc002yow.1	-						TIAM1_uc011adk.1_Intron|TIAM1_uc011adl.1_Intron|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																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	33015015	33015015	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33015015delT								TIAM1 (82725 upstream) : SOD1 (16920 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	33915176	33915176	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33915176delA								C21orf63 (27479 upstream) : TCP10L (31976 downstream)																																			---	---	---	---
TCP10L	140290	broad.mit.edu	37	21	33949091	33949091	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33949091delC	uc002ypw.3	-	5	757	c.641delG	c.(640-642)GGTfs	p.G214fs		NM_144659	NP_653260	Q9NV44	CU077_HUMAN	T-complex 10A-2	Error:Variant_position_missing_in_Q9NV44_after_alignment											0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	34263209	34263209	+	IGR	DEL	A	-	-	rs11406042		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34263209delA								C21orf62 (77156 upstream) : OLIG2 (135030 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	34498326	34498326	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34498326delT								OLIG1 (53599 upstream) : C21orf54 (39451 downstream)																																			---	---	---	---
CRYZL1	9946	broad.mit.edu	37	21	34981924	34981924	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34981924delT	uc011adw.1	-						DONSON_uc002ysn.1_Intron|CRYZL1_uc002ysr.1_Intron|CRYZL1_uc002yss.1_Intron|CRYZL1_uc002yst.1_Intron	NM_145858	NP_665857			crystallin, zeta-like 1						quinone cofactor metabolic process	cytosol	NADP binding|NADPH:quinone reductase activity|zinc ion binding				0																		---	---	---	---
CRYZL1	9946	broad.mit.edu	37	21	34987461	34987462	+	Intron	DEL	TT	-	-	rs10550201		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34987461_34987462delTT	uc011adw.1	-						DONSON_uc002ysn.1_Intron|CRYZL1_uc002ysr.1_Intron|CRYZL1_uc002yss.1_Intron|CRYZL1_uc002yst.1_Intron	NM_145858	NP_665857			crystallin, zeta-like 1						quinone cofactor metabolic process	cytosol	NADP binding|NADPH:quinone reductase activity|zinc ion binding				0																		---	---	---	---
ITSN1	6453	broad.mit.edu	37	21	35074100	35074101	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35074100_35074101delAA	uc002yta.1	+						DONSON_uc002ysn.1_Intron|ITSN1_uc002yth.3_Intron|ITSN1_uc002ysz.2_Intron|ITSN1_uc010gmg.2_Intron|ITSN1_uc010gmh.2_Intron|ITSN1_uc002ysw.2_Intron|ITSN1_uc010gmi.2_Intron|ITSN1_uc010gmj.2_Intron|ITSN1_uc002ysy.2_Intron|ITSN1_uc002ysx.2_Intron|ITSN1_uc002ytb.1_Intron	NM_003024	NP_003015			intersectin 1 isoform ITSN-l						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic vesicle endocytosis	cell junction|coated pit|cytosol|lamellipodium|synapse|synaptosome	calcium ion binding|proline-rich region binding|protein complex scaffold|Rho guanyl-nucleotide exchange factor activity			ovary(3)|skin(1)	4																		---	---	---	---
DONSON	29980	broad.mit.edu	37	21	35264172	35264172	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35264172delT	uc002ysn.1	-											Homo sapiens full length insert cDNA clone ZD90F06.						multicellular organismal development	nucleus				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
KCNE1	3753	broad.mit.edu	37	21	35880332	35880332	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35880332delT	uc010gmr.2	-						KCNE1_uc010gms.2_Intron|KCNE1_uc002yua.2_Intron	NM_000219	NP_000210			potassium voltage-gated channel, Isk-related						blood circulation|membrane depolarization|muscle contraction|sensory perception of sound	lysosome	delayed rectifier potassium channel activity|potassium channel regulator activity			ovary(2)	2					Indapamide(DB00808)													---	---	---	---
RUNX1	861	broad.mit.edu	37	21	37055537	37055537	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37055537delA	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	37097476	37097476	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37097476delT	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	37306123	37306123	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37306123delA	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	37518894	37518894	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37518894delT	uc002yvc.1	-						uc002yvd.1_Intron|uc002yvf.1_Intron					Homo sapiens mRNA expressed in placenta, clone IMAGE:139776.																														---	---	---	---
MORC3	23515	broad.mit.edu	37	21	37702485	37702485	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37702485delT	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																		---	---	---	---
MORC3	23515	broad.mit.edu	37	21	37726369	37726369	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37726369delA	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																		---	---	---	---
CHAF1B	8208	broad.mit.edu	37	21	37768302	37768302	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37768302delT	uc002yvj.2	+							NM_005441	NP_005432			chromatin assembly factor 1 subunit B						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|cytoplasm	chromatin binding|histone binding|unfolded protein binding			ovary(1)|skin(1)	2																		---	---	---	---
CLDN14	23562	broad.mit.edu	37	21	37910922	37910923	+	Intron	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37910922_37910923delAG	uc002yvn.1	-						CLDN14_uc002yvo.1_Intron	NM_001146078	NP_001139550			claudin 14						calcium-independent cell-cell adhesion|protein complex assembly|tight junction assembly	endoplasmic reticulum|integral to membrane|tight junction	identical protein binding|structural molecule activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	38398791	38398792	+	IGR	DEL	GA	-	-	rs111379498		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38398791_38398792delGA								DSCR6 (6835 upstream) : PIGP (38872 downstream)																																			---	---	---	---
TTC3	7267	broad.mit.edu	37	21	38569584	38569584	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38569584delA	uc002yvz.2	+						TTC3_uc002ywa.2_Intron|TTC3_uc002ywb.2_Intron|TTC3_uc010gnf.2_Intron|TTC3_uc002ywc.2_Intron	NM_001001894	NP_001001894			tetratricopeptide repeat domain 3						protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			skin(3)|ovary(2)|lung(2)|breast(2)	9		Myeloproliferative disorder(46;0.0412)																---	---	---	---
DYRK1A	1859	broad.mit.edu	37	21	38839103	38839103	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38839103delT	uc002ywk.2	+						DYRK1A_uc002ywg.1_Intron|DYRK1A_uc010gno.1_Intron|DYRK1A_uc002ywh.1_Intron|DYRK1A_uc002ywi.2_Intron|DYRK1A_uc002ywj.2_Intron|DYRK1A_uc002ywl.2_Intron|DYRK1A_uc002ywm.2_Intron	NM_001396	NP_001387			dual-specificity tyrosine-(Y)-phosphorylation						nervous system development|peptidyl-tyrosine phosphorylation|protein autophosphorylation	nuclear speck	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding|protein self-association|protein serine/threonine kinase activity			ovary(2)|lung(1)|breast(1)	4																		---	---	---	---
ERG	2078	broad.mit.edu	37	21	39824264	39824265	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39824264_39824265delAC	uc010gnw.2	-						ERG_uc002yxa.2_Intron|ERG_uc011aek.1_Intron|ERG_uc010gnv.2_Intron|ERG_uc010gnx.2_Intron|ERG_uc011ael.1_Intron|ERG_uc002yxb.2_Intron|ERG_uc011aem.1_Intron|ERG_uc002yxc.3_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)																---	---	---	---
BRWD1	54014	broad.mit.edu	37	21	40584804	40584804	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40584804delA	uc002yxk.1	-						BRWD1_uc010goc.1_Intron|BRWD1_uc002yxl.2_Intron|BRWD1_uc010god.1_Intron	NM_018963	NP_061836			bromodomain and WD repeat domain containing 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				skin(3)|ovary(1)	4		Prostate(19;8.44e-08)|all_epithelial(19;0.223)																---	---	---	---
SH3BGR	6450	broad.mit.edu	37	21	40866178	40866179	+	Intron	INS	-	TC	TC	rs57917957		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40866178_40866179insTC	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)														---	---	---	---
DSCAM	1826	broad.mit.edu	37	21	41759182	41759182	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41759182delA	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	41824655	41824655	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41824655delT	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	42263163	42263166	+	IGR	DEL	AAAC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42263163_42263166delAAAC								DSCAM (44124 upstream) : C21orf130 (250261 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	42484405	42484405	+	IGR	DEL	A	-	-	rs139503820		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42484405delA								DSCAM (265366 upstream) : C21orf130 (29022 downstream)																																			---	---	---	---
MX2	4600	broad.mit.edu	37	21	42766866	42766867	+	Intron	DEL	AG	-	-	rs72149533		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42766866_42766867delAG	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)																---	---	---	---
TMPRSS2	7113	broad.mit.edu	37	21	42847081	42847081	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42847081delA	uc002yzj.2	-						TMPRSS2_uc010gor.2_Intron|TMPRSS2_uc010gos.1_Intron	NM_005656	NP_005647			transmembrane protease, serine 2 isoform 2						proteolysis	cytoplasm|extracellular region|integral to plasma membrane	scavenger receptor activity|serine-type endopeptidase activity		TMPRSS2/ERG(2499)|TMPRSS2/ETV1(24)	prostate(2523)|central_nervous_system(1)	2524		Prostate(19;4.48e-07)|all_epithelial(19;0.031)						T	ERG|ETV1|ETV4|ETV5	prostate 								---	---	---	---
Unknown	0	broad.mit.edu	37	21	42937018	42937018	+	IGR	DEL	T	-	-	rs76655983		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42937018delT								TMPRSS2 (33975 upstream) : NCRNA00111 (162444 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	43198947	43198948	+	IGR	INS	-	TTTTTTTT	TTTTTTTT	rs59452985		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43198947_43198948insTTTTTTTT								RIPK4 (11698 upstream) : PRDM15 (19439 downstream)																																			---	---	---	---
PRDM15	63977	broad.mit.edu	37	21	43255983	43255984	+	Intron	DEL	CC	-	-	rs71999286		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43255983_43255984delCC	uc002yzq.1	-						PRDM15_uc002yzo.2_Intron|PRDM15_uc002yzp.2_Intron|PRDM15_uc002yzr.1_Intron	NM_022115	NP_071398			PR domain containing 15 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	43471178	43471179	+	IGR	INS	-	TG	TG	rs1977533		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43471178_43471179insTG								C21orf121 (26118 upstream) : UMODL1 (11889 downstream)																																			---	---	---	---
UMODL1	89766	broad.mit.edu	37	21	43504432	43504432	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43504432delG	uc002zaf.1	+						UMODL1_uc002zad.1_Intron|UMODL1_uc002zae.1_Intron|UMODL1_uc002zag.1_Intron|UMODL1_uc010gow.1_5'Flank|UMODL1_uc002zai.1_5'Flank|UMODL1_uc010gox.1_5'Flank|UMODL1_uc010goy.1_5'Flank|UMODL1_uc002zaj.1_5'Flank|UMODL1_uc010goz.1_5'Flank	NM_001004416	NP_001004416			uromodulin-like 1 isoform 1 precursor							cytoplasm|extracellular region|integral to membrane|plasma membrane	calcium ion binding|peptidase inhibitor activity			ovary(2)|skin(1)	3																		---	---	---	---
UBASH3A	53347	broad.mit.edu	37	21	43866400	43866400	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43866400delG	uc002zbe.2	+						UBASH3A_uc002zbf.2_Intron|UBASH3A_uc010gpc.2_Intron|UBASH3A_uc010gpd.2_Intron|UBASH3A_uc010gpe.2_Intron	NM_018961	NP_061834			ubiquitin associated and SH3 domain containing,							cytosol|nucleus				ovary(3)	3																		---	---	---	---
PDE9A	5152	broad.mit.edu	37	21	44126880	44126880	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44126880delC	uc002zbm.2	+						PDE9A_uc002zbn.2_Intron|PDE9A_uc002zbo.2_Intron|PDE9A_uc002zbp.2_Intron|PDE9A_uc002zbq.2_Intron|PDE9A_uc002zbs.2_Intron|PDE9A_uc002zbr.2_Intron|PDE9A_uc002zbt.2_Intron|PDE9A_uc002zbu.2_Intron|PDE9A_uc002zbv.2_Intron|PDE9A_uc002zbw.2_Intron|PDE9A_uc002zbx.2_Intron|PDE9A_uc002zby.2_Intron|PDE9A_uc002zbz.2_Intron|PDE9A_uc002zca.2_Intron|PDE9A_uc002zcb.2_Intron|PDE9A_uc002zcc.2_Intron|PDE9A_uc002zcd.2_Intron|PDE9A_uc002zce.2_Intron|PDE9A_uc002zcf.2_Intron|PDE9A_uc002zcg.2_Intron	NM_002606	NP_002597			phosphodiesterase 9A isoform a						platelet activation|signal transduction	cytosol|endoplasmic reticulum|Golgi apparatus|perinuclear region of cytoplasm|ruffle membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding|protein binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	44352012	44352013	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44352012_44352013insT								NDUFV3 (22240 upstream) : PKNOX1 (42630 downstream)																																			---	---	---	---
PKNOX1	5316	broad.mit.edu	37	21	44419594	44419595	+	Intron	INS	-	T	T	rs78725306	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44419594_44419595insT	uc002zcq.1	+						PKNOX1_uc002zcp.1_Intron|PKNOX1_uc011aex.1_Intron	NM_004571	NP_004562			PBX/knotted 1 homeobox 1								sequence-specific DNA binding			large_intestine(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	44600251	44600252	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44600251_44600252delTG								CRYAA (7338 upstream) : SIK1 (234146 downstream)																																			---	---	---	---
TRAPPC10	7109	broad.mit.edu	37	21	45448966	45448966	+	Intron	DEL	T	-	-	rs78423603		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45448966delT	uc002zea.2	+						TRAPPC10_uc010gpo.2_Intron|TRAPPC10_uc002zdz.2_Intron	NM_003274	NP_003265			trafficking protein particle complex 10						vesicle-mediated transport	Golgi apparatus|integral to membrane	binding|sodium ion transmembrane transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
TRAPPC10	7109	broad.mit.edu	37	21	45468344	45468344	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45468344delT	uc002zea.2	+						TRAPPC10_uc010gpo.2_Intron|TRAPPC10_uc002zdz.2_Intron	NM_003274	NP_003265			trafficking protein particle complex 10						vesicle-mediated transport	Golgi apparatus|integral to membrane	binding|sodium ion transmembrane transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
TRAPPC10	7109	broad.mit.edu	37	21	45499777	45499777	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45499777delA	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																		---	---	---	---
TRAPPC10	7109	broad.mit.edu	37	21	45500154	45500154	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45500154delT	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	46479033	46479033	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46479033delA								NCRNA00162 (54391 upstream) : C21orf122 (11840 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	46821275	46821276	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46821275_46821276delTT								LOC642852 (104007 upstream) : COL18A1 (3821 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	47607714	47607714	+	IGR	DEL	T	-	-	rs68162432		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47607714delT								C21orf56 (3341 upstream) : LSS (647 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	16947897	16947897	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16947897delA								OR11H1 (498093 upstream) : CCT8L2 (123751 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	17052838	17052838	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17052838delT								OR11H1 (603034 upstream) : CCT8L2 (18810 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	17236829	17236829	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17236829delT								psiTPTE22 (57308 upstream) : XKR3 (27484 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	17239409	17239410	+	IGR	INS	-	T	T	rs142595120	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17239409_17239410insT								psiTPTE22 (59888 upstream) : XKR3 (24903 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	18549997	18550000	+	IGR	DEL	AAAC	-	-	rs113471486		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18549997_18550000delAAAC								FLJ41941 (29263 upstream) : TUBA8 (10686 downstream)																																			---	---	---	---
DGCR5	26220	broad.mit.edu	37	22	18977070	18977075	+	Intron	DEL	TGTTTG	-	-	rs60823690		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18977070_18977075delTGTTTG	uc002zom.1	+						DGCR5_uc002zon.1_Intron	NR_002733				Homo sapiens mRNA for KIAA1647 protein, partial cds.												0																		---	---	---	---
HIRA	7290	broad.mit.edu	37	22	19370297	19370298	+	Intron	INS	-	C	C	rs113444553		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19370297_19370298insC	uc002zpf.1	-						HIRA_uc011agx.1_Intron|HIRA_uc010grn.1_Intron|HIRA_uc010gro.1_Intron|HIRA_uc010grp.2_Intron	NM_003325	NP_003316			HIR histone cell cycle regulation defective						chromatin modification|regulation of transcription from RNA polymerase II promoter	PML body	chromatin binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1	Colorectal(54;0.0993)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	19560063	19560063	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19560063delA								LOC150185 (5701 upstream) : SEPT5 (141924 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	20282787	20282787	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20282787delT								RTN4R (26971 upstream) : DGCR6L (19015 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	21003446	21003447	+	Intron	DEL	TT	-	-	rs4820551	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21003446_21003447delTT	uc002zsv.2	-											Homo sapiens, clone IMAGE:5171202, mRNA.																														---	---	---	---
SNAP29	9342	broad.mit.edu	37	22	21217602	21217603	+	Intron	INS	-	CCT	CCT	rs141661964	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21217602_21217603insCCT	uc011ahw.1	+							NM_004782	NP_004773			synaptosomal-associated protein 29						cellular membrane fusion|exocytosis|protein transport|vesicle targeting	cell junction|cytoplasm|nucleus|synapse|synaptosome	SNAP receptor activity				0	all_cancers(11;2.77e-25)|all_epithelial(7;8.92e-24)|Lung NSC(8;1.49e-15)|all_lung(8;2.54e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000592)|Lung(15;0.0117)															---	---	---	---
Unknown	0	broad.mit.edu	37	22	21316407	21316408	+	Intron	DEL	TT	-	-	rs78800285		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21316407_21316408delTT	uc002zti.1	+											Homo sapiens cDNA clone IMAGE:40134315.																														---	---	---	---
Unknown	0	broad.mit.edu	37	22	21606862	21606863	+	IGR	INS	-	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21606862_21606863insG								LOC400891 (188407 upstream) : POM121L8P (29851 downstream)																																			---	---	---	---
MAPK1	5594	broad.mit.edu	37	22	22138638	22138649	+	Intron	DEL	AAGAAAGAAAGG	-	-	rs72381351		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22138638_22138649delAAGAAAGAAAGG	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)													---	---	---	---
MAPK1	5594	broad.mit.edu	37	22	22142285	22142285	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22142285delA	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	22621380	22621381	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22621380_22621381insT	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	23124977	23124977	+	Intron	DEL	A	-	-	rs35482066		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23124977delA	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	23330961	23330961	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23330961delT								LOC96610 (65879 upstream) : RTDR1 (70633 downstream)																																			---	---	---	---
C22orf43	51233	broad.mit.edu	37	22	23953005	23953006	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23953005_23953006delTT	uc002zxf.2	-							NM_016449	NP_057533			hypothetical protein LOC51233											skin(1)	1																		---	---	---	---
SLC2A11	66035	broad.mit.edu	37	22	24199261	24199265	+	Intron	DEL	GGGGG	-	-	rs71184919		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24199261_24199265delGGGGG	uc002zyn.3	+						SLC2A11_uc002zyl.1_Intron|SLC2A11_uc002zym.3_Intron|SLC2A11_uc002zyo.3_Intron|SLC2A11_uc011ajc.1_5'UTR|SLC2A11_uc011ajd.1_5'Flank|SLC2A11_uc002zyp.3_5'Flank	NM_001024938	NP_001020109			glucose transporter protein 10 isoform c							integral to membrane|plasma membrane	sugar transmembrane transporter activity			ovary(1)	1																		---	---	---	---
SLC2A11	66035	broad.mit.edu	37	22	24208198	24208198	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24208198delA	uc002zyn.3	+						SLC2A11_uc002zyl.1_Intron|SLC2A11_uc002zym.3_Intron|SLC2A11_uc002zyo.3_Intron|SLC2A11_uc011ajc.1_Intron|SLC2A11_uc011ajd.1_Intron|SLC2A11_uc002zyp.3_Intron	NM_001024938	NP_001020109			glucose transporter protein 10 isoform c							integral to membrane|plasma membrane	sugar transmembrane transporter activity			ovary(1)	1																		---	---	---	---
SLC2A11	66035	broad.mit.edu	37	22	24216641	24216641	+	Intron	DEL	T	-	-	rs67463355		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24216641delT	uc002zyn.3	+						SLC2A11_uc002zyl.1_Intron|SLC2A11_uc002zym.3_Intron|SLC2A11_uc002zyo.3_Intron|SLC2A11_uc011ajc.1_Intron|SLC2A11_uc011ajd.1_Intron|SLC2A11_uc002zyp.3_Intron	NM_001024938	NP_001020109			glucose transporter protein 10 isoform c							integral to membrane|plasma membrane	sugar transmembrane transporter activity			ovary(1)	1																		---	---	---	---
CABIN1	23523	broad.mit.edu	37	22	24494250	24494250	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24494250delG	uc002zzi.1	+						CABIN1_uc002zzj.1_Intron|CABIN1_uc002zzl.1_Intron	NM_012295	NP_036427			calcineurin binding protein 1						cell surface receptor linked signaling pathway|chromatin modification	nucleus	protein phosphatase inhibitor activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5																		---	---	---	---
SUSD2	56241	broad.mit.edu	37	22	24578025	24578025	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24578025delC	uc002zzn.1	+							NM_019601	NP_062547			sushi domain containing 2 precursor						immune response	integral to membrane	polysaccharide binding|protein binding|scavenger receptor activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	24597536	24597537	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24597536_24597537delAA								SUSD2 (12462 upstream) : GGT5 (18086 downstream)																																			---	---	---	---
UPB1	51733	broad.mit.edu	37	22	24923770	24923771	+	Intron	DEL	AA	-	-	rs10550008		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24923770_24923771delAA	uc011ajt.1	+							NM_016327	NP_057411			beta-ureidopropionase						pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	cytosol	beta-ureidopropionase activity|metal ion binding			ovary(2)	2	Colorectal(2;0.0339)																	---	---	---	---
KIAA1671	85379	broad.mit.edu	37	22	25578291	25578316	+	Intron	DEL	TTTCTCTTCTTTCTTTCCTCCCTCCC	-	-	rs141443713	by1000genomes;by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25578291_25578316delTTTCTCTTCTTTCTTTCCTCCCTCCC	uc003abn.2	+						KIAA1671_uc003abl.2_Intron	NM_001145206	NP_001138678			hypothetical protein LOC85379											lung(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	25704927	25704928	+	IGR	INS	-	GGTGTGTGCG	GGTGTGTGCG	rs71322746		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25704927_25704928insGGTGTGTGCG								CRYBB2 (77091 upstream) : IGLL3 (8960 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	25710462	25710462	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25710462delA								CRYBB2 (82626 upstream) : IGLL3 (3426 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	25856137	25856137	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25856137delT	uc003abt.2	+						uc003abu.2_Intron|uc003abv.2_Intron					Homo sapiens cDNA clone IMAGE:3542716, partial cds.																														---	---	---	---
ADRBK2	157	broad.mit.edu	37	22	26070916	26070917	+	Intron	DEL	AA	-	-	rs74681758		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26070916_26070917delAA	uc003abx.3	+						ADRBK2_uc010gux.2_Intron|ADRBK2_uc003abw.2_Intron|ADRBK2_uc003aby.3_Intron	NM_005160	NP_005151			beta-adrenergic receptor kinase 2								ATP binding|beta-adrenergic receptor kinase activity|signal transducer activity			lung(3)|ovary(2)|stomach(1)|central_nervous_system(1)	7					Adenosine triphosphate(DB00171)													---	---	---	---
SEZ6L	23544	broad.mit.edu	37	22	26741992	26741992	+	Intron	DEL	T	-	-	rs62703760		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26741992delT	uc003acb.2	+						SEZ6L_uc003acc.2_Intron|SEZ6L_uc011akc.1_Intron|SEZ6L_uc003acd.2_Intron|SEZ6L_uc011akd.1_Intron|SEZ6L_uc003ace.2_Intron|SEZ6L_uc003acf.1_Intron|SEZ6L_uc010gvc.1_Intron|SEZ6L_uc011ake.1_5'Flank	NM_021115	NP_066938			seizure related 6 homolog (mouse)-like							endoplasmic reticulum membrane|integral to membrane				ovary(4)|central_nervous_system(1)|pancreas(1)	6																		---	---	---	---
TPST2	8459	broad.mit.edu	37	22	26936862	26936862	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26936862delG	uc003acv.2	-	2	903	c.735delC	c.(733-735)CCCfs	p.P245fs	TPST2_uc003acw.2_Frame_Shift_Del_p.P245fs|TPST2_uc003acx.2_Frame_Shift_Del_p.P245fs|TPST2_uc011akf.1_Frame_Shift_Del_p.P245fs	NM_003595	NP_003586	O60704	TPST2_HUMAN	tyrosylprotein sulfotransferase 2	245	Lumenal (Potential).				peptidyl-tyrosine sulfation	endoplasmic reticulum|Golgi membrane|integral to membrane|membrane fraction	protein-tyrosine sulfotransferase activity			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	27417194	27417195	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27417194_27417195insT								MIAT (302245 upstream) : MN1 (727071 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27439014	27439014	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27439014delT								MIAT (324065 upstream) : MN1 (705252 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27765221	27765222	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27765221_27765222delTT								MIAT (650272 upstream) : MN1 (379044 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27810209	27810209	+	IGR	DEL	C	-	-	rs35429398		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27810209delC								MIAT (695260 upstream) : MN1 (334057 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	28004007	28004008	+	IGR	DEL	TG	-	-	rs66504365		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28004007_28004008delTG								MIAT (889058 upstream) : MN1 (140258 downstream)																																			---	---	---	---
PITPNB	23760	broad.mit.edu	37	22	28286346	28286346	+	Intron	DEL	T	-	-	rs67180422		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28286346delT	uc003adk.2	-						PITPNB_uc011akh.1_Intron|PITPNB_uc003adl.2_Intron	NM_012399	NP_036531			phosphatidylinositol transfer protein, beta						lipid metabolic process|transport	Golgi apparatus	lipid binding			skin(1)	1																		---	---	---	---
NF2	4771	broad.mit.edu	37	22	29997191	29997192	+	5'Flank	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29997191_29997192insT	uc003age.3	+						NF2_uc003afy.3_5'Flank|NF2_uc003afz.3_5'Flank|NF2_uc003agf.3_5'Flank|NF2_uc003agb.3_5'Flank|NF2_uc003agc.3_5'Flank|NF2_uc003agd.3_5'Flank|NF2_uc003agg.3_5'Flank|NF2_uc003aga.3_5'Flank|NF2_uc003agh.3_5'Flank|NF2_uc003agi.3_5'Flank|NF2_uc003agj.3_5'Flank	NM_000268	NP_000259			neurofibromin 2 isoform 1						actin cytoskeleton organization|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of cell-matrix adhesion|negative regulation of DNA replication|negative regulation of tyrosine phosphorylation of Stat3 protein|negative regulation of tyrosine phosphorylation of Stat5 protein|positive regulation of stress fiber assembly|regulation of hippo signaling cascade|Schwann cell proliferation	cytoskeleton|early endosome|extrinsic to membrane|filopodium membrane|nucleolus|perinuclear region of cytoplasm|ruffle membrane	cytoskeletal protein binding|protein binding	p.?(1)		meninges(372)|soft_tissue(284)|central_nervous_system(20)|kidney(10)|pleura(9)|skin(7)|large_intestine(5)|breast(5)|urinary_tract(3)|thyroid(2)|endometrium(2)|ovary(2)|lung(2)|stomach(2)|bone(2)|pituitary(1)	728								D|Mis|N|F|S|O		meningioma|acoustic neuroma|renal 	meningioma|acoustic neuroma			Neurofibromatosis_type_2				---	---	---	---
UQCR10	29796	broad.mit.edu	37	22	30165486	30165486	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	30172316	30172316	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30172316delA								UQCR10 (5914 upstream) : ASCC2 (12287 downstream)																																			---	---	---	---
ASCC2	84164	broad.mit.edu	37	22	30218612	30218613	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30218612_30218613delTT	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)															---	---	---	---
HORMAD2	150280	broad.mit.edu	37	22	30512202	30512202	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30512202delG	uc003agy.2	+							NM_152510	NP_689723			HORMA domain containing 2						meiosis|mitosis	chromosome|nucleus					0			Epithelial(10;0.125)															---	---	---	---
HORMAD2	150280	broad.mit.edu	37	22	30522160	30522160	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30522160delT	uc003agy.2	+							NM_152510	NP_689723			HORMA domain containing 2						meiosis|mitosis	chromosome|nucleus					0			Epithelial(10;0.125)															---	---	---	---
OSBP2	23762	broad.mit.edu	37	22	31214271	31214271	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31214271delT	uc003aiy.1	+						OSBP2_uc011ala.1_Intron|OSBP2_uc010gwc.1_Intron|OSBP2_uc003aix.1_Intron|OSBP2_uc011alb.1_Intron|OSBP2_uc003aiz.1_Intron|OSBP2_uc003aja.1_Intron	NM_030758	NP_110385			oxysterol binding protein 2 isoform a						lipid transport	membrane	lipid binding			breast(1)|skin(1)	2																		---	---	---	---
C22orf27	150291	broad.mit.edu	37	22	31320542	31320542	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31320542delA	uc003ajc.2	+						C22orf27_uc003ajd.2_Intron	NR_026920				Homo sapiens cDNA FLJ35801 fis, clone TESTI2005937.												0																		---	---	---	---
MORC2	22880	broad.mit.edu	37	22	31331657	31331658	+	Intron	INS	-	GC	GC	rs141214223	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31331657_31331658insGC	uc003aje.1	-							NM_014941	NP_055756			MORC family CW-type zinc finger 2								ATP binding|zinc ion binding			ovary(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	31425568	31425568	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31425568delT								TUG1 (50191 upstream) : SMTN (51737 downstream)																																			---	---	---	---
RNF185	91445	broad.mit.edu	37	22	31593902	31593902	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31593902delA	uc003akb.2	+						RNF185_uc010gwh.2_Intron|RNF185_uc011alm.1_Intron|RNF185_uc003akc.2_Intron|RNF185_uc003ake.2_Intron	NM_152267	NP_689480			ring finger protein 185 isoform 1							integral to membrane	zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	32068251	32068252	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32068251_32068252delTT								PISD (10050 upstream) : C22orf30 (3990 downstream)																																			---	---	---	---
C22orf30	253143	broad.mit.edu	37	22	32099784	32099785	+	Intron	DEL	TT	-	-	rs35530740		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32099784_32099785delTT	uc003alp.3	-						C22orf30_uc003alo.1_Intron|C22orf30_uc010gwj.1_Intron	NM_173566	NP_775837			hypothetical protein LOC253143												0																OREG0003534	type=REGULATORY REGION|Gene=AK123082|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
DEPDC5	9681	broad.mit.edu	37	22	32213783	32213783	+	Intron	DEL	T	-	-	rs76514013		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32213783delT	uc003als.2	+						DEPDC5_uc011als.1_Intron|DEPDC5_uc011alu.1_Intron|DEPDC5_uc011alv.1_Intron|DEPDC5_uc003alt.2_Intron|DEPDC5_uc003alu.2_5'Flank|DEPDC5_uc003alv.2_5'Flank|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																		---	---	---	---
DEPDC5	9681	broad.mit.edu	37	22	32291681	32291681	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32291681delT	uc003als.2	+						DEPDC5_uc011als.1_Intron|DEPDC5_uc011alu.1_Intron|DEPDC5_uc011alv.1_Intron|DEPDC5_uc003alt.2_Intron|DEPDC5_uc003alu.2_Intron|DEPDC5_uc003alv.2_Intron|DEPDC5_uc003alw.2_Intron|DEPDC5_uc011alx.1_Intron|DEPDC5_uc010gwk.2_Intron|DEPDC5_uc011aly.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	32700128	32700128	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32700128delT								SLC5A4 (48810 upstream) : RFPL3 (50744 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	32746894	32746894	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32746894delA								SLC5A4 (95576 upstream) : RFPL3 (3978 downstream)																																			---	---	---	---
SYN3	8224	broad.mit.edu	37	22	33324966	33324966	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33324966delA	uc003amx.2	-						SYN3_uc003amy.2_Intron|SYN3_uc003amz.2_Intron	NM_003490	NP_003481			synapsin III isoform IIIa						neurotransmitter secretion	cell junction|synaptic vesicle membrane	ATP binding|ligase activity			skin(1)	1																		---	---	---	---
SYN3	8224	broad.mit.edu	37	22	33355538	33355538	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33355538delA	uc003amx.2	-						SYN3_uc003amy.2_Intron|SYN3_uc003amz.2_Intron	NM_003490	NP_003481			synapsin III isoform IIIa						neurotransmitter secretion	cell junction|synaptic vesicle membrane	ATP binding|ligase activity			skin(1)	1																		---	---	---	---
SYN3	8224	broad.mit.edu	37	22	33368833	33368833	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33368833delA	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	33868036	33868036	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33868036delA	uc003and.3	-						LARGE_uc011amd.1_Intron|LARGE_uc003ane.3_Intron|LARGE_uc010gwp.2_Intron|LARGE_uc011ame.1_Intron|LARGE_uc011amf.1_Intron|LARGE_uc010gwq.1_Intron	NM_004737	NP_004728			like-glycosyltransferase						glycosphingolipid biosynthetic process|muscle cell homeostasis|N-acetylglucosamine metabolic process|protein glycosylation	integral to Golgi membrane	acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(1;0.219)																---	---	---	---
LARGE	9215	broad.mit.edu	37	22	34257376	34257377	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34257376_34257377delAC	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	34333677	34333678	+	IGR	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34333677_34333678delGT								LARGE (15093 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	34928307	34928307	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34928307delA								LARGE (609723 upstream) : ISX (533822 downstream)																																			---	---	---	---
RBM9	23543	broad.mit.edu	37	22	36199195	36199196	+	Intron	DEL	AC	-	-	rs112148294		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36199195_36199196delAC	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|RBM9_uc003aop.3_Intron	NM_001082578	NP_001076047			RNA binding motif protein 9 isoform 5						estrogen receptor signaling pathway|mRNA processing|negative regulation of transcription, DNA-dependent|regulation of cell proliferation|RNA splicing	cytoplasm|nucleus	nucleotide binding|RNA binding|transcription corepressor activity|transcription factor binding				0																		---	---	---	---
RBM9	23543	broad.mit.edu	37	22	36276294	36276294	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36276294delG	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																		---	---	---	---
RBM9	23543	broad.mit.edu	37	22	36394432	36394432	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36394432delT	uc003aon.3	-						RBM9_uc003aoo.3_Intron	NM_001082578	NP_001076047			RNA binding motif protein 9 isoform 5						estrogen receptor signaling pathway|mRNA processing|negative regulation of transcription, DNA-dependent|regulation of cell proliferation|RNA splicing	cytoplasm|nucleus	nucleotide binding|RNA binding|transcription corepressor activity|transcription factor binding				0																		---	---	---	---
APOL3	80833	broad.mit.edu	37	22	36546762	36546763	+	Intron	DEL	CA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36546762_36546763delCA	uc003aot.2	-						APOL3_uc003aoq.2_Intron|APOL3_uc003aor.2_Intron|APOL3_uc003aos.2_Intron|APOL3_uc003aou.2_Intron|APOL3_uc003aov.2_Intron	NM_145640	NP_663615			apolipoprotein L3 isoform 1						inflammatory response|lipoprotein metabolic process|positive regulation of I-kappaB kinase/NF-kappaB cascade	cytoplasm|extracellular region	lipid binding|lipid transporter activity|signal transducer activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	36577729	36577730	+	IGR	DEL	TG	-	-	rs71771701		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36577729_36577730delTG								APOL3 (15504 upstream) : APOL4 (7448 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	36675766	36675766	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36675766delA								APOL1 (12190 upstream) : MYH9 (1558 downstream)																																			---	---	---	---
MYH9	4627	broad.mit.edu	37	22	36773463	36773464	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36773463_36773464delAA	uc003apg.2	-							NM_002473	NP_002464			myosin, heavy polypeptide 9, non-muscle						actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	11								T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				---	---	---	---
IL2RB	3560	broad.mit.edu	37	22	37539957	37539960	+	Intron	DEL	GTGC	-	-	rs148571987	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37539957_37539960delGTGC	uc003aqv.1	-							NM_000878	NP_000869			interleukin 2 receptor beta precursor						interspecies interaction between organisms|positive regulation of survival gene product expression|protein complex assembly	external side of plasma membrane|integral to plasma membrane	interleukin-2 receptor activity				0					Aldesleukin(DB00041)|Basiliximab(DB00074)|Daclizumab(DB00111)|Denileukin diftitox(DB00004)													---	---	---	---
LGALS1	3956	broad.mit.edu	37	22	38072084	38072084	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38072084delC	uc003atn.2	+							NM_002305	NP_002296			galectin-1						apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of apoptosis	cytoplasm|extracellular space|proteinaceous extracellular matrix	galactoside binding|signal transducer activity				0	Melanoma(58;0.0574)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	38178865	38178866	+	IGR	DEL	TT	-	-	rs71687583		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38178865_38178866delTT								TRIOBP (6303 upstream) : H1F0 (22248 downstream)																																			---	---	---	---
C22orf23	84645	broad.mit.edu	37	22	38343084	38343084	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38343084delA	uc003auj.1	-						C22orf23_uc003auk.1_Intron	NM_032561	NP_115950			hypothetical protein LOC84645												0	Melanoma(58;0.045)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	39319576	39319576	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39319576delA								CBX6 (51318 upstream) : APOBEC3A (33951 downstream)																																			---	---	---	---
APOBEC3D	140564	broad.mit.edu	37	22	39421774	39421774	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39421774delC	uc011aoe.1	+						APOBEC3D_uc011aof.1_Intron|APOBEC3D_uc003awu.3_Intron|APOBEC3D_uc003awt.3_Intron|APOBEC3D_uc010gxu.2_Intron	NM_152426	NP_689639			apolipoprotein B mRNA editing enzyme, catalytic						negative regulation of transposition		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines|zinc ion binding				0	Melanoma(58;0.04)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	39460584	39460584	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39460584delA								APOBEC3F (8611 upstream) : APOBEC3G (12441 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	39644319	39644319	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39644319delT								PDGFB (3362 upstream) : RPL3 (64569 downstream)																																			---	---	---	---
ENTHD1	150350	broad.mit.edu	37	22	40239624	40239624	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40239624delA	uc003ayg.2	-							NM_152512	NP_689725			ENTH domain containing 1											ovary(2)|skin(1)	3	Melanoma(58;0.0749)																	---	---	---	---
TNRC6B	23112	broad.mit.edu	37	22	40536232	40536232	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40536232delA	uc003aym.2	+							NM_001024843	NP_001020014			trinucleotide repeat containing 6B isoform 3						gene silencing by RNA|regulation of translation	cytoplasmic mRNA processing body	nucleotide binding|RNA binding				0																		---	---	---	---
TNRC6B	23112	broad.mit.edu	37	22	40572127	40572129	+	5'Flank	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40572127_40572129delTTT	uc011aor.1	+						TNRC6B_uc003aym.2_Intron|TNRC6B_uc003ayn.3_5'Flank	NM_001162501	NP_001155973			trinucleotide repeat containing 6B isoform 1						gene silencing by RNA|regulation of translation	cytoplasmic mRNA processing body	nucleotide binding|RNA binding				0																		---	---	---	---
TNRC6B	23112	broad.mit.edu	37	22	40658233	40658233	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40658233delT	uc011aor.1	+						TNRC6B_uc003aym.2_Intron|TNRC6B_uc003ayn.3_Intron|TNRC6B_uc003ayo.2_5'Flank	NM_001162501	NP_001155973			trinucleotide repeat containing 6B isoform 1						gene silencing by RNA|regulation of translation	cytoplasmic mRNA processing body	nucleotide binding|RNA binding				0																		---	---	---	---
MKL1	57591	broad.mit.edu	37	22	40916418	40916419	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40916418_40916419delTT	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	40954802	40954802	+	Intron	DEL	T	-	-	rs67311117		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40954802delT	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	40968011	40968011	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40968011delA	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								---	---	---	---
EP300	2033	broad.mit.edu	37	22	41565470	41565470	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41565470delT	uc003azl.3	+							NM_001429	NP_001420			E1A binding protein p300						apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia	centrosome|histone acetyltransferase complex	androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1)	64								T| N|F|Mis|O	MLL|RUNXBP2	colorectal|breast|pancreatic|AML|ALL|DLBCL				Rubinstein-Taybi_syndrome				---	---	---	---
CHADL	150356	broad.mit.edu	37	22	41631879	41631879	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41631879delT	uc003azq.3	-						CHADL_uc010gyj.2_Intron	NM_138481	NP_612490			chondroadherin-like precursor							proteinaceous extracellular matrix					0																		---	---	---	---
PPPDE2	27351	broad.mit.edu	37	22	42000737	42000738	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42000737_42000738delAA	uc003ban.1	-						PPPDE2_uc011apb.1_Intron	NM_015704	NP_056519			PPPDE peptidase domain containing 2												0																		---	---	---	---
C22orf46	79640	broad.mit.edu	37	22	42087764	42087765	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42087764_42087765delTT	uc003bax.1	+						NHP2L1_uc003bav.2_5'Flank|NHP2L1_uc003baw.2_5'Flank	NM_001142964	NP_001136436			hypothetical protein LOC79640							extracellular region					0																		---	---	---	---
C22orf32	91689	broad.mit.edu	37	22	42477174	42477175	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42477174_42477175delTT	uc003bca.2	+							NM_033318	NP_201575			hypothetical protein LOC91689 precursor							integral to membrane|mitochondrion				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	42495655	42495655	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42495655delT	uc003bcc.1	+						uc003bcd.1_Intron					Homo sapiens cDNA FLJ41636 fis, clone FEBRA1000022.																														---	---	---	---
TCF20	6942	broad.mit.edu	37	22	42575382	42575382	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42575382delA	uc003bcj.1	-						TCF20_uc003bck.1_Intron|TCF20_uc003bnt.2_Intron	NM_005650	NP_005641			transcription factor 20 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(4)|skin(1)	5																		---	---	---	---
SERHL	94009	broad.mit.edu	37	22	42898666	42898666	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42898666delC	uc011apm.1	+						SERHL_uc011apl.1_Intron					RecName: Full=Serine hydrolase-like protein;          EC=3.1.-.-;												0																		---	---	---	---
SERHL	94009	broad.mit.edu	37	22	42902251	42902253	+	Intron	DEL	AAA	-	-	rs74349192		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42902251_42902253delAAA	uc011apm.1	+						SERHL_uc011apl.1_Intron					RecName: Full=Serine hydrolase-like protein;          EC=3.1.-.-;												0																		---	---	---	---
EFCAB6	64800	broad.mit.edu	37	22	44013982	44013982	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44013982delA	uc003bdy.1	-						EFCAB6_uc003bdz.1_Intron|EFCAB6_uc010gzi.1_Intron|EFCAB6_uc010gzj.1_Intron	NM_022785	NP_073622			CAP-binding protein complex interacting protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	calcium ion binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	7		Ovarian(80;0.0247)|all_neural(38;0.025)																---	---	---	---
EFCAB6	64800	broad.mit.edu	37	22	44131949	44131949	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44131949delT	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)																---	---	---	---
PNPLA5	150379	broad.mit.edu	37	22	44279691	44279691	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44279691delA	uc003beg.2	-						PNPLA5_uc011aqc.1_Intron|PNPLA5_uc003beh.2_Intron	NM_138814	NP_620169			patatin-like phospholipase domain containing 5						lipid catabolic process		hydrolase activity				0		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)																---	---	---	---
SAMM50	25813	broad.mit.edu	37	22	44362243	44362243	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44362243delT	uc003bej.2	+						SAMM50_uc011aqd.1_Intron	NM_015380	NP_056195			sorting and assembly machinery component 50						protein import into mitochondrial outer membrane	integral to membrane|integral to membrane of membrane fraction|mitochondrial sorting and assembly machinery complex	protein binding			skin(1)	1		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)																---	---	---	---
PARVB	29780	broad.mit.edu	37	22	44462701	44462703	+	Intron	DEL	TCT	-	-	rs7288356		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44462701_44462703delTCT	uc003ben.2	+						PARVB_uc003bem.2_Intron|PARVB_uc010gzn.2_Intron|PARVB_uc003beo.2_5'Flank	NM_013327	NP_037459			parvin, beta isoform b						cell adhesion|cell junction assembly	cytoskeleton|cytosol|focal adhesion	actin binding				0		Ovarian(80;0.0246)|all_neural(38;0.0423)																---	---	---	---
Unknown	0	broad.mit.edu	37	22	44956007	44956008	+	IGR	INS	-	A	A	rs149463576	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44956007_44956008insA								LDOC1L (62002 upstream) : NCRNA00207 (9211 downstream)																																			---	---	---	---
PHF21B	112885	broad.mit.edu	37	22	45392536	45392537	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45392536_45392537delAC	uc003bfn.2	-						PHF21B_uc003bfm.2_Intron|PHF21B_uc011aqk.1_Intron|PHF21B_uc011aql.1_Intron|PHF21B_uc011aqm.1_Intron	NM_138415	NP_612424			PHD finger protein 21B isoform 1								zinc ion binding			ovary(2)|skin(1)	3		all_neural(38;0.00802)|Glioma(61;0.0353)|Ovarian(80;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0203)														---	---	---	---
ATXN10	25814	broad.mit.edu	37	22	46087773	46087773	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46087773delA	uc003bgm.1	+						ATXN10_uc011aqt.1_Intron|ATXN10_uc003bgn.1_Intron	NM_013236	NP_037368			ataxin 10						cell death|neuron projection development	dendrite|neuronal cell body|perinuclear region of cytoplasm				ovary(1)|kidney(1)	2		Ovarian(80;0.00973)|all_neural(38;0.0417)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0223)														---	---	---	---
WNT7B	7477	broad.mit.edu	37	22	46325764	46325771	+	Intron	DEL	CCACTCAT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46325764_46325771delCCACTCAT	uc003bgo.2	-						WNT7B_uc010haa.2_Intron	NM_058238	NP_478679			wingless-type MMTV integration site family,						activation of JUN kinase activity|anterior/posterior pattern formation|axis specification|axonogenesis|canonical Wnt receptor signaling pathway|cell-cell signaling|cellular response to retinoic acid|central nervous system vasculogenesis|chorio-allantoic fusion|developmental growth involved in morphogenesis|embryonic placenta morphogenesis|establishment or maintenance of polarity of embryonic epithelium|fibroblast proliferation|forebrain regionalization|inner medullary collecting duct development|lens fiber cell development|lobar bronchus development|lung epithelium development|lung morphogenesis|lung-associated mesenchyme development|mammary gland epithelium development|metanephric collecting duct development|metanephric loop of Henle development|metanephros morphogenesis|negative regulation of smoothened signaling pathway|outer medullary collecting duct development|oxygen homeostasis|positive regulation of JNK cascade|positive regulation of osteoblast differentiation|renal inner medulla development|renal outer medulla development|stem cell proliferation|synapse organization|trachea cartilage morphogenesis|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|frizzled binding|signal transducer activity			lung(1)	1		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
WNT7B	7477	broad.mit.edu	37	22	46370090	46370090	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46370090delT	uc003bgo.2	-						WNT7B_uc010haa.2_5'Flank	NM_058238	NP_478679			wingless-type MMTV integration site family,						activation of JUN kinase activity|anterior/posterior pattern formation|axis specification|axonogenesis|canonical Wnt receptor signaling pathway|cell-cell signaling|cellular response to retinoic acid|central nervous system vasculogenesis|chorio-allantoic fusion|developmental growth involved in morphogenesis|embryonic placenta morphogenesis|establishment or maintenance of polarity of embryonic epithelium|fibroblast proliferation|forebrain regionalization|inner medullary collecting duct development|lens fiber cell development|lobar bronchus development|lung epithelium development|lung morphogenesis|lung-associated mesenchyme development|mammary gland epithelium development|metanephric collecting duct development|metanephric loop of Henle development|metanephros morphogenesis|negative regulation of smoothened signaling pathway|outer medullary collecting duct development|oxygen homeostasis|positive regulation of JNK cascade|positive regulation of osteoblast differentiation|renal inner medulla development|renal outer medulla development|stem cell proliferation|synapse organization|trachea cartilage morphogenesis|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|frizzled binding|signal transducer activity			lung(1)	1		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
LOC400931	400931	broad.mit.edu	37	22	46478264	46478264	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46478264delT	uc003bgr.3	+											SubName: Full=FLJ27365 protein, isoform CRA_a; SubName: Full=Novel transcript;												0																		---	---	---	---
TRMU	55687	broad.mit.edu	37	22	46745994	46745994	+	Intron	DEL	T	-	-	rs72489274		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46745994delT	uc003bhp.2	+						TRMU_uc011arb.1_Intron|TRMU_uc003bhq.2_Intron|TRMU_uc003bhs.2_Intron|TRMU_uc003bhr.2_Intron|TRMU_uc003bht.2_Intron|TRMU_uc003bhu.2_Intron|TRMU_uc003bhv.2_Intron	NM_018006	NP_060476			tRNA 5-methylaminomethyl-2-thiouridylate							mitochondrion	ATP binding|sulfurtransferase activity|tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase activity|tRNA binding			ovary(1)	1		Ovarian(80;0.00965)|Breast(42;0.0194)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00449)|LUAD - Lung adenocarcinoma(64;0.248)														---	---	---	---
TBC1D22A	25771	broad.mit.edu	37	22	47495347	47495348	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47495347_47495348delTT	uc003bib.2	+						TBC1D22A_uc010haf.2_Intron|TBC1D22A_uc003bic.2_Intron|TBC1D22A_uc003bie.2_Intron|TBC1D22A_uc003bid.2_Intron|TBC1D22A_uc010hag.2_Intron|TBC1D22A_uc003bif.2_Intron	NM_014346	NP_055161			TBC1 domain family, member 22A							intracellular	protein homodimerization activity|Rab GTPase activator activity			ovary(1)	1		all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231)														---	---	---	---
Unknown	0	broad.mit.edu	37	22	47643742	47643742	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47643742delT								TBC1D22A (74020 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	47809633	47809633	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47809633delT								TBC1D22A (239911 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	48300910	48300910	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48300910delT								TBC1D22A (731188 upstream) : FAM19A5 (584378 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	48385749	48385749	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48385749delT								TBC1D22A (816027 upstream) : FAM19A5 (499539 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	48833896	48833898	+	IGR	DEL	AAC	-	-	rs35847141		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48833896_48833898delAAC								None (None upstream) : FAM19A5 (51390 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	49492067	49492068	+	IGR	DEL	CA	-	-	rs66968582		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49492067_49492068delCA								FAM19A5 (344325 upstream) : C22orf34 (316108 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	49535165	49535166	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49535165_49535166delTG								FAM19A5 (387423 upstream) : C22orf34 (273010 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	49547848	49547848	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49547848delG								FAM19A5 (400106 upstream) : C22orf34 (260328 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	49780626	49780627	+	IGR	INS	-	TT	TT			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49780626_49780627insTT								FAM19A5 (632884 upstream) : C22orf34 (27549 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	50419412	50419412	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50419412delT								PIM3 (61693 upstream) : IL17REL (13530 downstream)																																			---	---	---	---
IL17REL	400935	broad.mit.edu	37	22	50452338	50452339	+	5'Flank	INS	-	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50452338_50452339insC	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)														---	---	---	---
TTLL8	164714	broad.mit.edu	37	22	50495944	50495944	+	5'Flank	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50495944delG	uc011ark.1	-							NM_001080447	NP_001073916			tubulin tyrosine ligase-like family, member 8											ovary(2)	2		all_cancers(38;3.44e-07)|all_epithelial(38;2.44e-06)|all_lung(38;0.00141)|Breast(42;0.00519)|Lung NSC(38;0.0199)|Ovarian(80;0.142)|Lung SC(80;0.162)		READ - Rectum adenocarcinoma(2;0.000882)|Colorectal(2;0.00311)|BRCA - Breast invasive adenocarcinoma(115;0.226)														---	---	---	---
SHANK3	85358	broad.mit.edu	37	22	51127948	51127948	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:51127948delT	uc003bne.1	+							NM_001080420	NP_001073889			SH3 and multiple ankyrin repeat domains 3											central_nervous_system(1)	1		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)														---	---	---	---
Unknown	0	broad.mit.edu	37	X	941062	941063	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:941062_941063insT								SHOX (320917 upstream) : CRLF2 (373824 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	1206631	1206632	+	IGR	INS	-	CAG	CAG			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1206631_1206632insCAG								SHOX (586486 upstream) : CRLF2 (108255 downstream)																																			---	---	---	---
ASMT	438	broad.mit.edu	37	X	1730002	1730002	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1730002delT	uc004cqd.2	+							NM_004043	NP_004034			acetylserotonin O-methyltransferase						melatonin biosynthetic process|translation	cytosol	acetylserotonin O-methyltransferase activity|S-methyltransferase activity			skin(1)	1		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)																---	---	---	---
Unknown	0	broad.mit.edu	37	X	1806755	1806755	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1806755delA								ASMT (44782 upstream) : DHRSX (330802 downstream)																																			---	---	---	---
GYG2	8908	broad.mit.edu	37	X	2778180	2778180	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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	2815880	2815880	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2815880delG								GYG2 (15019 upstream) : ARSD (6132 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	3137278	3137278	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:3137278delT								ARSF (106531 upstream) : MXRA5 (89333 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	3730116	3730116	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:3730116delA								PRKX (98455 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	3976879	3976880	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:3976879_3976880insA								PRKX (345218 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	4859093	4859093	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:4859093delA								None (None upstream) : NLGN4X (948991 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	5456614	5456615	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:5456614_5456615delTT								None (None upstream) : NLGN4X (351469 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	6422855	6422855	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:6422855delT								NLGN4X (276149 upstream) : VCX3A (28805 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	6807691	6807691	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:6807691delC								VCX3A (354532 upstream) : HDHD1A (159270 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	6828698	6828698	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:6828698delA								VCX3A (375539 upstream) : HDHD1A (138263 downstream)																																			---	---	---	---
STS	412	broad.mit.edu	37	X	7191821	7191821	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7191821delA	uc004cry.3	+							NM_000351	NP_000342			steryl-sulfatase precursor						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	7339049	7339049	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7339049delT								STS (66369 upstream) : VCX (471254 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	7568621	7568621	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7568621delT								STS (295941 upstream) : VCX (241682 downstream)																																			---	---	---	---
VCX2	51480	broad.mit.edu	37	X	8141682	8141683	+	5'Flank	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:8141682_8141683delTC	uc004csb.2	-							NM_016378	NP_057462			variable charge, X-linked 2												0		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)																---	---	---	---
FAM9A	171482	broad.mit.edu	37	X	8764320	8764320	+	Frame_Shift_Del	DEL	T	-	-	rs1985393		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:8764320delT	uc004csg.2	-	6	588	c.477delA	c.(475-477)AAAfs	p.K159fs		NM_174951	NP_777611	Q8IZU1	FAM9A_HUMAN	family with sequence similarity 9, member A	159						nucleolus					0		Hepatocellular(5;0.219)																---	---	---	---
Unknown	0	broad.mit.edu	37	X	9341738	9341738	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9341738delA								FAM9B (209091 upstream) : TBL1X (89597 downstream)																																			---	---	---	---
TBL1X	6907	broad.mit.edu	37	X	9544160	9544160	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9544160delC	uc010ndq.2	+						TBL1X_uc004csq.3_Intron|TBL1X_uc010ndr.2_Intron|TBL1X_uc004csr.2_Intron	NM_001139466	NP_001132938			transducin beta-like 1X isoform a						canonical Wnt receptor signaling pathway|cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|proteasomal ubiquitin-dependent protein catabolic process|sensory perception of sound|transcription, DNA-dependent	spindle microtubule|transcriptional repressor complex	beta-catenin binding|histone binding|protein C-terminus binding|protein domain specific binding|transcription corepressor activity|transcription factor binding|transcription regulatory region DNA binding			ovary(1)	1		Hepatocellular(5;0.000888)																---	---	---	---
GPR143	4935	broad.mit.edu	37	X	9721715	9721715	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9721715delC	uc004cst.1	-							NM_000273	NP_000264			G protein-coupled receptor 143						calcium-mediated signaling using intracellular calcium source|eye pigment biosynthetic process|melanosome organization|melanosome transport|phosphatidylinositol-mediated signaling|regulation of calcium-mediated signaling|visual perception	apical plasma membrane|Golgi apparatus|integral to membrane|lysosomal membrane|melanosome membrane|membrane fraction	dopamine binding|L-DOPA receptor activity|protein binding|tyrosine binding			ovary(1)	1		Hepatocellular(5;0.000888)																---	---	---	---
Unknown	0	broad.mit.edu	37	X	9942087	9942087	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9942087delT								SHROOM2 (24606 upstream) : WWC3 (41708 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	10288253	10288253	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:10288253delA								CLCN4 (82556 upstream) : MID1 (125344 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	10934241	10934241	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:10934241delT								MID1 (82432 upstream) : HCCS (195174 downstream)																																			---	---	---	---
FRMPD4	9758	broad.mit.edu	37	X	12420369	12420369	+	Intron	DEL	C	-	-	rs11297309		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12420369delC	uc004cuz.1	+						FRMPD4_uc011mij.1_Intron	NM_014728	NP_055543			FERM and PDZ domain containing 4						positive regulation of synapse structural plasticity	cytoskeleton|dendritic spine	phosphatidylinositol-4,5-bisphosphate binding|protein binding			central_nervous_system(5)|ovary(3)|skin(2)|large_intestine(1)|lung(1)|pancreas(1)	13																		---	---	---	---
FRMPD4	9758	broad.mit.edu	37	X	12575946	12575947	+	Intron	INS	-	T	T	rs148225814		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12575946_12575947insT	uc004cuz.1	+						FRMPD4_uc011mij.1_Intron	NM_014728	NP_055543			FERM and PDZ domain containing 4						positive regulation of synapse structural plasticity	cytoskeleton|dendritic spine	phosphatidylinositol-4,5-bisphosphate binding|protein binding			central_nervous_system(5)|ovary(3)|skin(2)|large_intestine(1)|lung(1)|pancreas(1)	13																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	13133005	13133006	+	IGR	DEL	AG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13133005_13133006delAG								FAM9C (70205 upstream) : ATXN3L (203764 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	13225754	13225754	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13225754delC								FAM9C (162954 upstream) : ATXN3L (111016 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	13364317	13364317	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13364317delA								ATXN3L (25799 upstream) : EGFL6 (223424 downstream)																																			---	---	---	---
TRAPPC2	6399	broad.mit.edu	37	X	13737929	13737929	+	Intron	DEL	C	-	-	rs3214139		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13737929delC	uc010nek.1	-						TRAPPC2_uc010nel.1_Intron|TRAPPC2_uc010nem.1_Intron	NM_001011658	NP_001011658			trafficking protein particle complex 2 isoform						ER to Golgi vesicle-mediated transport	intracellular					0																		---	---	---	---
GPM6B	2824	broad.mit.edu	37	X	13906849	13906849	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13906849delA	uc004cvx.2	-						GPM6B_uc011min.1_Intron|GPM6B_uc004cwa.2_Intron	NM_001001994	NP_001001994			glycoprotein M6B isoform 4						cell differentiation|nervous system development	integral to membrane					0																		---	---	---	---
GEMIN8	54960	broad.mit.edu	37	X	14039512	14039512	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14039512delA	uc004cwb.2	-						GEMIN8_uc004cwc.2_Intron|GEMIN8_uc004cwd.2_Intron	NM_017856	NP_060326			gem (nuclear organelle) associated protein 8						spliceosomal snRNP assembly	Cajal body|cytoplasm|SMN complex|spliceosomal complex	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	14347294	14347294	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14347294delA								GEMIN8 (299259 upstream) : GLRA2 (200126 downstream)																																			---	---	---	---
GLRA2	2742	broad.mit.edu	37	X	14748756	14748756	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14748756delA	uc010nep.2	+	10					GLRA2_uc010neq.2_3'UTR|GLRA2_uc004cwe.3_3'UTR|GLRA2_uc011mio.1_3'UTR|GLRA2_uc011mip.1_3'UTR	NM_001118885	NP_001112357			glycine receptor, alpha 2 isoform A						neuropeptide signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|glycine binding|receptor activity|transmitter-gated ion channel activity			ovary(1)|lung(1)	2	Hepatocellular(33;0.128)				Ethanol(DB00898)|Glycine(DB00145)													---	---	---	---
Unknown	0	broad.mit.edu	37	X	15727014	15727014	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15727014delA								CA5BP (5539 upstream) : CA5B (29398 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	16132243	16132243	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16132243delA								AP1S2 (259143 upstream) : GRPR (9181 downstream)																																			---	---	---	---
SYAP1	94056	broad.mit.edu	37	X	16754276	16754276	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16754276delT	uc004cxp.2	+						SYAP1_uc004cxo.2_Intron|SYAP1_uc011miv.1_Intron	NM_032796	NP_116185			SYAP1 protein											skin(1)	1	Hepatocellular(33;0.0997)																	---	---	---	---
SYAP1	94056	broad.mit.edu	37	X	16773453	16773453	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16773453delT	uc004cxp.2	+						SYAP1_uc004cxo.2_Intron|SYAP1_uc011miv.1_Intron	NM_032796	NP_116185			SYAP1 protein											skin(1)	1	Hepatocellular(33;0.0997)																	---	---	---	---
RBBP7	5931	broad.mit.edu	37	X	16879319	16879319	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16879319delA	uc004cxt.2	-						RBBP7_uc004cxs.1_Intron|RBBP7_uc004cxu.2_Intron|RBBP7_uc010nez.2_5'Flank	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)																	---	---	---	---
NHS	4810	broad.mit.edu	37	X	17724611	17724612	+	Intron	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17724611_17724612delAC	uc004cxx.2	+						NHS_uc011mix.1_Intron|NHS_uc004cxy.2_Intron|NHS_uc004cxz.2_Intron|NHS_uc004cya.2_Intron	NM_198270	NP_938011			Nance-Horan syndrome protein isoform 1							nucleus				skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	Hepatocellular(33;0.183)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	17935932	17935932	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17935932delT								RAI2 (56475 upstream) : BEND2 (245121 downstream)																																			---	---	---	---
SCML2	10389	broad.mit.edu	37	X	18273234	18273234	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18273234delA	uc004cyl.2	-						SCML2_uc004cyk.3_Intron|SCML2_uc010nfd.1_Intron|SCML2_uc011miz.1_Intron|SCML2_uc010nfc.2_Intron	NM_006089	NP_006080			sex comb on midleg-like 2						anatomical structure morphogenesis	PcG protein complex	DNA binding|sequence-specific DNA binding transcription factor activity				0	Hepatocellular(33;0.183)																	---	---	---	---
CDKL5	6792	broad.mit.edu	37	X	18597856	18597856	+	Intron	DEL	A	-	-	rs12013924		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18597856delA	uc004cym.2	+						CDKL5_uc004cyn.2_Intron	NM_003159	NP_003150			cyclin-dependent kinase-like 5						neuron migration|positive regulation of axon extension|positive regulation of dendrite morphogenesis|positive regulation of Rac GTPase activity|protein autophosphorylation	dendrite cytoplasm|dendritic growth cone|nucleus	ATP binding|cyclin-dependent protein kinase activity|Rac GTPase binding			ovary(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)|skin(1)	6	Hepatocellular(33;0.183)																	---	---	---	---
SH3KBP1	30011	broad.mit.edu	37	X	19816370	19816370	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19816370delT	uc004czm.2	-						SH3KBP1_uc004czl.2_Intron	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	20387192	20387192	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:20387192delT								RPS6KA3 (101669 upstream) : None (None downstream)																																			---	---	---	---
PHEX	5251	broad.mit.edu	37	X	22060933	22060933	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22060933delA	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	22384402	22384403	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22384402_22384403delTT								ZNF645 (91828 upstream) : DDX53 (633684 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	22461577	22461577	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22461577delA								ZNF645 (169003 upstream) : DDX53 (556510 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	22462468	22462468	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22462468delT								ZNF645 (169894 upstream) : DDX53 (555619 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	23199455	23199455	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23199455delT								DDX53 (179251 upstream) : PTCHD1 (153530 downstream)																																			---	---	---	---
ACOT9	23597	broad.mit.edu	37	X	23725862	23725863	+	Intron	DEL	AC	-	-	rs5970599		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23725862_23725863delAC	uc004dap.2	-						ACOT9_uc004dan.2_5'Flank|ACOT9_uc004dao.2_Intron|ACOT9_uc004daq.2_Intron|ACOT9_uc004dar.2_Intron|ACOT9_uc011mjt.1_Intron|ACOT9_uc004das.2_Intron	NM_001033583	NP_001028755			acyl-Coenzyme A thioesterase 2, mitochondrial						acyl-CoA metabolic process	mitochondrion	acetyl-CoA hydrolase activity|carboxylesterase activity			ovary(2)|pancreas(1)	3																		---	---	---	---
APOO	79135	broad.mit.edu	37	X	23878797	23878797	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23878797delT	uc004dax.2	-						APOO_uc004daw.2_Intron|APOO_uc004day.3_Intron	NM_024122	NP_077027			apolipoprotein O precursor						lipid transport	high-density lipoprotein particle|integral to membrane|low-density lipoprotein particle|very-low-density lipoprotein particle					0																		---	---	---	---
KLHL15	80311	broad.mit.edu	37	X	24038714	24038714	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24038714delA	uc004dba.3	-							NM_030624	NP_085127			kelch-like 15											ovary(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	24383621	24383621	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24383621delT								FAM48B1 (81 upstream) : PDK3 (99723 downstream)																																			---	---	---	---
PDK3	5165	broad.mit.edu	37	X	24517162	24517162	+	Intron	DEL	T	-	-	rs113531183		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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																		---	---	---	---
PCYT1B	9468	broad.mit.edu	37	X	24624827	24624827	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24624827delA	uc004dbi.2	-						PCYT1B_uc004dbk.3_Intron|PCYT1B_uc004dbj.2_Intron	NM_004845	NP_004836			choline phosphate cytidylyltransferase 1 beta							endoplasmic reticulum	choline-phosphate cytidylyltransferase activity				0					Choline(DB00122)													---	---	---	---
POLA1	5422	broad.mit.edu	37	X	25007547	25007548	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:25007547_25007548delTT	uc004dbl.2	+							NM_016937	NP_058633			DNA-directed DNA polymerase alpha 1						cell proliferation|DNA replication checkpoint|DNA replication, synthesis of RNA primer|DNA-dependent DNA replication initiation|double-strand break repair via nonhomologous end joining|interspecies interaction between organisms|lagging strand elongation|leading strand elongation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|cytoplasm|nuclear envelope|nuclear matrix|nucleolus|nucleoplasm	chromatin binding|DNA-directed DNA polymerase activity|metal ion binding|nucleoside binding			ovary(2)|skin(1)	3					Clofarabine(DB00631)|Fludarabine(DB01073)													---	---	---	---
Unknown	0	broad.mit.edu	37	X	25130765	25130765	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:25130765delT								ARX (96700 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	25521894	25521895	+	IGR	INS	-	TT	TT			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:25521894_25521895insTT								ARX (487829 upstream) : MAGEB18 (634568 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	25683040	25683040	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:25683040delA								ARX (648975 upstream) : MAGEB18 (473423 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	25740642	25740642	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:25740642delA								ARX (706577 upstream) : MAGEB18 (415821 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	27946491	27946492	+	IGR	DEL	AT	-	-	rs114503428	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:27946491_27946492delAT								MAGEB10 (105729 upstream) : DCAF8L1 (49618 downstream)																																			---	---	---	---
IL1RAPL1	11141	broad.mit.edu	37	X	29909633	29909633	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:29909633delA	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																		---	---	---	---
GK	2710	broad.mit.edu	37	X	30688716	30688717	+	Intron	DEL	TT	-	-	rs148330109		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30688716_30688717delTT	uc004dch.3	+						GK_uc010ngj.2_Intron|GK_uc004dci.3_Intron|GK_uc011mjz.1_Intron|GK_uc011mka.1_Intron|GK_uc010ngk.2_Intron	NM_203391	NP_976325			glycerol kinase isoform a						glycerol-3-phosphate metabolic process|triglyceride biosynthetic process	cytosol|mitochondrial outer membrane	ATP binding|glycerol kinase activity			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	30838495	30838496	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30838495_30838496insT								GK (89771 upstream) : TAB3 (7064 downstream)																																			---	---	---	---
DMD	1756	broad.mit.edu	37	X	31233363	31233364	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31233363_31233364delTT	uc004dda.1	-						DMD_uc004dcq.1_Intron|DMD_uc004dcr.1_Intron|DMD_uc004dcs.1_Intron|DMD_uc004dct.1_Intron|DMD_uc004dcu.1_Intron|DMD_uc004dcv.1_Intron|DMD_uc004dcw.2_Intron|DMD_uc004dcx.2_Intron|DMD_uc004dcz.2_Intron|DMD_uc004dcy.1_Intron|DMD_uc004ddb.1_Intron|DMD_uc004dcm.1_Intron|DMD_uc004dcn.1_Intron|DMD_uc004dco.1_Intron|DMD_uc004dcp.1_Intron|DMD_uc011mkb.1_Intron|DMD_uc010ngm.2_Intron	NM_004006	NP_003997			dystrophin Dp427m isoform						muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)																---	---	---	---
DMD	1756	broad.mit.edu	37	X	31464593	31464593	+	Intron	DEL	A	-	-	rs35964020		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31464593delA	uc004dda.1	-						DMD_uc004dcq.1_Intron|DMD_uc004dcr.1_Intron|DMD_uc004dcs.1_Intron|DMD_uc004dct.1_Intron|DMD_uc004dcu.1_Intron|DMD_uc004dcv.1_Intron|DMD_uc004dcw.2_Intron|DMD_uc004dcx.2_Intron|DMD_uc004dcz.2_Intron|DMD_uc004dcy.1_Intron|DMD_uc004ddb.1_Intron	NM_004006	NP_003997			dystrophin Dp427m isoform						muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)																---	---	---	---
DMD	1756	broad.mit.edu	37	X	32349020	32349020	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:32349020delA	uc004dda.1	-						DMD_uc004dcw.2_Intron|DMD_uc004dcx.2_Intron|DMD_uc004dcz.2_Intron|DMD_uc004dcy.1_Intron|DMD_uc004ddb.1_Intron|DMD_uc010ngo.1_Intron	NM_004006	NP_003997			dystrophin Dp427m isoform						muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)																---	---	---	---
Unknown	0	broad.mit.edu	37	X	34735503	34735514	+	IGR	DEL	TTTTTTTTTTTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:34735503_34735514delTTTTTTTTTTTT								TMEM47 (60098 upstream) : FAM47B (225417 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	36229987	36229987	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:36229987delT								CXorf59 (66800 upstream) : CXorf30 (24064 downstream)																																			---	---	---	---
PRRG1	5638	broad.mit.edu	37	X	37220593	37220594	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37220593_37220594delAA	uc004ddn.2	+						PRRG1_uc004ddo.2_Intron	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	37540090	37540091	+	IGR	DEL	GT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37540090_37540091delGT								LANCL3 (3341 upstream) : XK (5042 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	37733525	37733525	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37733525delT								DYNLT3 (26636 upstream) : CXorf27 (116545 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	38348945	38348945	+	IGR	DEL	A	-	-	rs112990408		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38348945delA								OTC (68243 upstream) : TSPAN7 (71786 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	38386328	38386328	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38386328delA								OTC (105626 upstream) : TSPAN7 (34403 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	38958287	38958287	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38958287delC								MID1IP1 (292506 upstream) : BCOR (952214 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	38981348	38981349	+	IGR	DEL	GA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38981348_38981349delGA								MID1IP1 (315567 upstream) : BCOR (929152 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	39313649	39313649	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:39313649delT								MID1IP1 (647868 upstream) : BCOR (596852 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	39489963	39489963	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:39489963delT								MID1IP1 (824182 upstream) : BCOR (420538 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	39545531	39545538	+	IGR	DEL	GAAGGAAG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:39545531_39545538delGAAGGAAG								MID1IP1 (879750 upstream) : BCOR (364963 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	39552867	39552868	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:39552867_39552868delTT								MID1IP1 (887086 upstream) : BCOR (357633 downstream)																																			---	---	---	---
BCOR	54880	broad.mit.edu	37	X	39962634	39962634	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:39962634delC	uc004dep.3	-						BCOR_uc004deo.3_Intron	NM_001123383	NP_001116855			BCL-6 interacting corepressor isoform a						heart development|histone H2A monoubiquitination|negative regulation of bone mineralization|negative regulation of histone H3-K36 methylation|negative regulation of histone H3-K4 methylation|negative regulation of tooth mineralization|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|palate development|specification of axis polarity|transcription, DNA-dependent	nucleus	heat shock protein binding|histone deacetylase binding|transcription corepressor activity|transcription factor binding|transcription regulatory region DNA binding			ovary(2)|kidney(1)|central_nervous_system(1)	4																		---	---	---	---
BCOR	54880	broad.mit.edu	37	X	39983529	39983529	+	Intron	DEL	T	-	-	rs5902246		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:39983529delT	uc004dep.3	-						BCOR_uc004deo.3_Intron	NM_001123383	NP_001116855			BCL-6 interacting corepressor isoform a						heart development|histone H2A monoubiquitination|negative regulation of bone mineralization|negative regulation of histone H3-K36 methylation|negative regulation of histone H3-K4 methylation|negative regulation of tooth mineralization|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|palate development|specification of axis polarity|transcription, DNA-dependent	nucleus	heat shock protein binding|histone deacetylase binding|transcription corepressor activity|transcription factor binding|transcription regulatory region DNA binding			ovary(2)|kidney(1)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	40298248	40298249	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40298248_40298249delTT								BCOR (261666 upstream) : ATP6AP2 (141967 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	40298421	40298421	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40298421delA								BCOR (261839 upstream) : ATP6AP2 (141795 downstream)																																			---	---	---	---
ATP6AP2	10159	broad.mit.edu	37	X	40465111	40465111	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40465111delA	uc004det.2	+	9					ATP6AP2_uc010nhc.2_RNA|ATP6AP2_uc011mkl.1_3'UTR|ATP6AP2_uc011mkm.1_3'UTR|ATP6AP2_uc011mkn.1_3'UTR|ATP6AP2_uc004deu.1_3'UTR	NM_005765	NP_005756			ATPase, H+ transporting, lysosomal accessory						angiotensin maturation|positive regulation of transforming growth factor-beta1 production|regulation of MAPKKK cascade	external side of plasma membrane|integral to membrane	protein binding|receptor activity				0																		---	---	---	---
NYX	60506	broad.mit.edu	37	X	41313574	41313574	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41313574delT	uc004dfh.2	+						NYX_uc011mku.1_Intron	NM_022567	NP_072089			nyctalopin precursor						response to stimulus|visual perception	intracellular|proteinaceous extracellular matrix				lung(2)	2																		---	---	---	---
CASK	8573	broad.mit.edu	37	X	41769475	41769476	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41769475_41769476delAA	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	41945158	41945158	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41945158delA								CASK (162871 upstream) : PPP1R2P9 (691461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	42307356	42307356	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:42307356delC								CASK (525069 upstream) : PPP1R2P9 (329263 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	42480869	42480871	+	IGR	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:42480869_42480871delAAA								CASK (698582 upstream) : PPP1R2P9 (155748 downstream)																																			---	---	---	---
EFHC2	80258	broad.mit.edu	37	X	44152657	44152657	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44152657delT	uc004dgb.3	-							NM_025184	NP_079460			EF-hand domain (C-terminal) containing 2								calcium ion binding			breast(3)|ovary(2)|central_nervous_system(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	44463553	44463553	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44463553delT								FUNDC1 (61332 upstream) : DUSP21 (239696 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	44629991	44629991	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44629991delT								FUNDC1 (227770 upstream) : DUSP21 (73258 downstream)																																			---	---	---	---
CXorf36	79742	broad.mit.edu	37	X	45026573	45026573	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:45026573delA	uc004dgg.2	-						CXorf36_uc004dgi.3_Intron	NM_176819	NP_789789			hypothetical protein LOC79742 isoform 1							extracellular region				lung(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	45184966	45184967	+	IGR	DEL	TA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:45184966_45184967delTA								CXorf36 (124820 upstream) : MIR221 (420618 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	45319730	45319730	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:45319730delT								CXorf36 (259584 upstream) : MIR221 (285855 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	46174309	46174311	+	IGR	DEL	TTT	-	-	rs10677219		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46174309_46174311delTTT								MIR222 (567779 upstream) : ZNF673 (132313 downstream)																																			---	---	---	---
ZNF674	641339	broad.mit.edu	37	X	46363474	46363474	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46363474delA	uc004dgr.2	-						ZNF674_uc011mlg.1_Intron	NM_001039891	NP_001034980			zinc finger family member 674 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(2)	2																		---	---	---	---
SLC9A7	84679	broad.mit.edu	37	X	46614121	46614122	+	Intron	INS	-	A	A	rs61006481		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46614121_46614122insA	uc004dgu.1	-						SLC9A7_uc004dgv.1_Intron	NM_032591	NP_115980			solute carrier family 9, member 7						regulation of pH	Golgi membrane|integral to membrane|recycling endosome membrane|trans-Golgi network	potassium:hydrogen antiporter activity|protein homodimerization activity|sodium:hydrogen antiporter activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	46755713	46755713	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46755713delT								RP2 (13924 upstream) : PHF16 (16023 downstream)																																			---	---	---	---
PHF16	9767	broad.mit.edu	37	X	46808381	46808381	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46808381delT	uc004dgx.2	+						PHF16_uc004dgy.2_Intron	NM_001077445	NP_001070913			PHD finger protein 16						histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding				0																		---	---	---	---
USP11	8237	broad.mit.edu	37	X	47090862	47090864	+	5'Flank	DEL	AAA	-	-	rs73201996	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47090862_47090864delAAA	uc004dhp.2	+							NM_004651	NP_004642			ubiquitin specific peptidase 11						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	47294985	47294985	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47294985delT								ZNF157 (21887 upstream) : ZNF41 (10577 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	47622830	47622830	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47622830delT								LOC100133957 (103054 upstream) : ZNF81 (73471 downstream)																																			---	---	---	---
SLC38A5	92745	broad.mit.edu	37	X	48331037	48331037	+	5'Flank	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48331037delA	uc010nid.2	-							NM_033518	NP_277053			solute carrier family 38, member 5						cellular nitrogen compound metabolic process|ion transport	integral to membrane|plasma membrane				ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	48635378	48635378	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48635378delA								GLOD5 (3316 upstream) : GATA1 (9604 downstream)																																			---	---	---	---
TIMM17B	10245	broad.mit.edu	37	X	48754309	48754310	+	Intron	INS	-	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48754309_48754310insC	uc004dlc.1	-						PQBP1_uc004dle.2_5'Flank|PQBP1_uc004dlf.2_5'Flank|PQBP1_uc004dlg.2_5'Flank|PQBP1_uc004dld.2_5'Flank|PQBP1_uc004dlh.2_5'Flank|PQBP1_uc004dli.2_5'Flank|PQBP1_uc004dlj.1_5'Flank|PQBP1_uc004dln.2_5'Flank|PQBP1_uc010nih.2_5'Flank|PQBP1_uc010nii.2_5'Flank|PQBP1_uc004dlk.2_5'Flank|PQBP1_uc004dll.2_5'Flank|PQBP1_uc004dlm.2_5'Flank|PQBP1_uc010nij.2_5'Flank|TIMM17B_uc004dla.1_Intron|TIMM17B_uc004dlb.1_Intron	NM_005834	NP_005825			translocase of inner mitochondrial membrane 17						protein targeting to mitochondrion	integral to membrane|microtubule cytoskeleton|mitochondrial inner membrane presequence translocase complex	P-P-bond-hydrolysis-driven protein transmembrane transporter activity			ovary(1)	1																		---	---	---	---
CACNA1F	778	broad.mit.edu	37	X	49089284	49089286	+	Intron	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49089284_49089286delTTT	uc004dnb.2	-						CACNA1F_uc010nip.2_Intron|CCDC22_uc011mna.1_5'Flank|CCDC22_uc004dnc.1_5'Flank|CCDC22_uc004dnd.1_5'Flank	NM_005183	NP_005174			calcium channel, voltage-dependent, L type,						axon guidance|detection of light stimulus involved in visual perception	voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			breast(3)|ovary(1)|kidney(1)|skin(1)	6					Verapamil(DB00661)													---	---	---	---
CLCN5	1184	broad.mit.edu	37	X	49716859	49716859	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49716859delA	uc004dor.1	+						CLCN5_uc004doq.1_Intron	NM_001127899	NP_001121371			chloride channel 5 isoform a						excretion	apical part of cell|endosome membrane|Golgi membrane|integral to plasma membrane	antiporter activity|ATP binding			ovary(2)|lung(1)|central_nervous_system(1)	4	Ovarian(276;0.236)																	---	---	---	---
DGKK	139189	broad.mit.edu	37	X	50206381	50206382	+	Intron	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50206381_50206382delTC	uc010njr.1	-							NM_001013742	NP_001013764			diacylglycerol kinase kappa						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|diacylglycerol metabolic process|intracellular signal transduction|platelet activation|response to oxidative stress	cytoplasm|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)	2	Ovarian(276;0.236)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	50308781	50308783	+	IGR	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50308781_50308783delAAA								DGKK (95044 upstream) : SHROOM4 (25860 downstream)																																			---	---	---	---
SHROOM4	57477	broad.mit.edu	37	X	50529449	50529449	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50529449delT	uc004dpe.2	-						SHROOM4_uc004dpd.3_Intron	NM_020717	NP_065768			shroom family member 4						actin filament organization|brain development|cell morphogenesis|cognition	apical plasma membrane|basal plasma membrane|internal side of plasma membrane|nucleus	actin filament binding			upper_aerodigestive_tract(1)	1	Ovarian(276;0.236)																	---	---	---	---
SHROOM4	57477	broad.mit.edu	37	X	50535509	50535510	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50535509_50535510delAA	uc004dpe.2	-						SHROOM4_uc004dpd.3_Intron	NM_020717	NP_065768			shroom family member 4						actin filament organization|brain development|cell morphogenesis|cognition	apical plasma membrane|basal plasma membrane|internal side of plasma membrane|nucleus	actin filament binding			upper_aerodigestive_tract(1)	1	Ovarian(276;0.236)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	51355223	51355223	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:51355223delA								NUDT11 (115764 upstream) : GSPT2 (131274 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	53166785	53166785	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53166785delA	uc004dry.2	+											full-length cDNA clone CS0DC007YA11 of Neuroblastoma Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	X	53478133	53478133	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53478133delT								HSD17B10 (16810 upstream) : HUWE1 (80939 downstream)																																			---	---	---	---
HUWE1	10075	broad.mit.edu	37	X	53643042	53643042	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53643042delT	uc004dsp.2	-							NM_031407	NP_113584			HECT, UBA and WWE domain containing 1						base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	DNA binding|protein binding|ubiquitin-protein ligase activity			ovary(8)|large_intestine(4)|breast(4)|kidney(1)	17																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	54085955	54085955	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54085955delT								PHF8 (14559 upstream) : FAM120C (8804 downstream)																																			---	---	---	---
WNK3	65267	broad.mit.edu	37	X	54265637	54265638	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54265637_54265638delAA	uc004dtd.1	-						WNK3_uc004dtc.1_Intron	NM_001002838	NP_001002838			WNK lysine deficient protein kinase 3 isoform 2						intracellular protein kinase cascade|positive regulation of establishment of protein localization in plasma membrane|positive regulation of peptidyl-threonine phosphorylation|positive regulation of rubidium ion transmembrane transporter activity|positive regulation of rubidium ion transport|positive regulation of sodium ion transmembrane transporter activity|positive regulation of sodium ion transport|protein autophosphorylation	adherens junction|tight junction	ATP binding|protein binding|protein serine/threonine kinase activity|rubidium ion transmembrane transporter activity|sodium ion transmembrane transporter activity			lung(4)|ovary(3)|kidney(2)|central_nervous_system(2)	11																		---	---	---	---
WNK3	65267	broad.mit.edu	37	X	54303151	54303153	+	Intron	DEL	TTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54303151_54303153delTTT	uc004dtd.1	-						WNK3_uc004dtc.1_Intron	NM_001002838	NP_001002838			WNK lysine deficient protein kinase 3 isoform 2						intracellular protein kinase cascade|positive regulation of establishment of protein localization in plasma membrane|positive regulation of peptidyl-threonine phosphorylation|positive regulation of rubidium ion transmembrane transporter activity|positive regulation of rubidium ion transport|positive regulation of sodium ion transmembrane transporter activity|positive regulation of sodium ion transport|protein autophosphorylation	adherens junction|tight junction	ATP binding|protein binding|protein serine/threonine kinase activity|rubidium ion transmembrane transporter activity|sodium ion transmembrane transporter activity			lung(4)|ovary(3)|kidney(2)|central_nervous_system(2)	11																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	54927355	54927355	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54927355delA								MAGED2 (84910 upstream) : TRO (19894 downstream)																																			---	---	---	---
FAAH2	158584	broad.mit.edu	37	X	57360947	57360947	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:57360947delA	uc004dvc.2	+							NM_174912	NP_777572			fatty acid amide hydrolase 2							integral to membrane	carbon-nitrogen ligase activity, with glutamine as amido-N-donor|hydrolase activity			ovary(3)	3															HNSCC(52;0.14)			---	---	---	---
Unknown	0	broad.mit.edu	37	X	57867039	57867040	+	IGR	DEL	GT	-	-	rs148644686		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:57867039_57867040delGT								ZXDB (243133 upstream) : ZXDA (67158 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	61714751	61714751	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:61714751delA								None (None upstream) : SPIN4 (852357 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	61793987	61793987	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:61793987delT								None (None upstream) : SPIN4 (773121 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	61816108	61816108	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:61816108delA								None (None upstream) : SPIN4 (751000 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	62274539	62274539	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:62274539delT								None (None upstream) : SPIN4 (292569 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	62318265	62318267	+	IGR	DEL	AAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:62318265_62318267delAAA								None (None upstream) : SPIN4 (248841 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	63887014	63887015	+	IGR	INS	-	A	A	rs113901927		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:63887014_63887015insA								MTMR8 (271703 upstream) : ZC4H2 (249247 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	64548402	64548402	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:64548402delT								ZC4H2 (293809 upstream) : ZC3H12B (160304 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	64587594	64587594	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:64587594delT								ZC4H2 (333001 upstream) : ZC3H12B (121112 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	65368713	65368713	+	IGR	DEL	A	-	-	rs72182547		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:65368713delA								VSIG4 (108746 upstream) : HEPH (13950 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	66176406	66176407	+	IGR	DEL	AC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:66176406_66176407delAC								EDA2R (317298 upstream) : AR (587467 downstream)																																			---	---	---	---
OPHN1	4983	broad.mit.edu	37	X	67283052	67283052	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67283052delA	uc004dww.3	-						OPHN1_uc011mpg.1_Intron	NM_002547	NP_002538			oligophrenin 1						axon guidance|endocytosis|filopodium assembly|small GTPase mediated signal transduction|substrate-dependent cell migration, cell extension	axon|cell junction|cytosol|dendritic spine|synapse	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(2)	2																		---	---	---	---
OPHN1	4983	broad.mit.edu	37	X	67324555	67324555	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67324555delA	uc004dww.3	-						OPHN1_uc011mpg.1_Intron	NM_002547	NP_002538			oligophrenin 1						axon guidance|endocytosis|filopodium assembly|small GTPase mediated signal transduction|substrate-dependent cell migration, cell extension	axon|cell junction|cytosol|dendritic spine|synapse	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	67847622	67847622	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67847622delT								YIPF6 (95322 upstream) : STARD8 (19889 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	68346019	68346019	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:68346019delT								EFNB1 (279990 upstream) : PJA1 (34563 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	68700894	68700894	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:68700894delA								PJA1 (315554 upstream) : FAM155B (24184 downstream)																																			---	---	---	---
EDA	1896	broad.mit.edu	37	X	68853536	68853537	+	Intron	INS	-	A	A	rs72539285		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:68853536_68853537insA	uc004dxs.2	+						EDA_uc004dxr.2_Intron|EDA_uc011mpj.1_Intron|EDA_uc004dxn.1_Intron|EDA_uc004dxm.1_Intron|EDA_uc004dxp.1_Intron|EDA_uc004dxq.1_Intron	NM_001399	NP_001390			ectodysplasin A isoform EDA-A1						cell differentiation|ectoderm development|immune response|positive regulation of NF-kappaB transcription factor activity|signal transduction	collagen|cytoskeleton|membrane fraction	tumor necrosis factor receptor binding			ovary(2)|large_intestine(1)	3																		---	---	---	---
EDA	1896	broad.mit.edu	37	X	69241450	69241450	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69241450delA	uc004dxs.2	+						EDA_uc004dxr.2_Intron|EDA_uc011mpj.1_Intron	NM_001399	NP_001390			ectodysplasin A isoform EDA-A1						cell differentiation|ectoderm development|immune response|positive regulation of NF-kappaB transcription factor activity|signal transduction	collagen|cytoskeleton|membrane fraction	tumor necrosis factor receptor binding			ovary(2)|large_intestine(1)	3																		---	---	---	---
KIF4A	24137	broad.mit.edu	37	X	69594238	69594239	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69594238_69594239insA	uc004dyg.2	+						KIF4A_uc010nkw.2_Intron|KIF4A_uc004dyf.1_Intron	NM_012310	NP_036442			kinesin family member 4						anterograde axon cargo transport|axon guidance|blood coagulation|organelle organization	chromosome|cytosol|midbody|nuclear matrix|spindle microtubule	ATP binding|DNA binding|microtubule motor activity|protein binding			ovary(4)	4																		---	---	---	---
GDPD2	54857	broad.mit.edu	37	X	69644740	69644740	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69644740delC	uc004dyh.2	+						GDPD2_uc010nkx.1_Intron|GDPD2_uc010nky.1_Intron|GDPD2_uc011mpk.1_Intron|GDPD2_uc011mpl.1_Intron|GDPD2_uc011mpm.1_Intron	NM_017711	NP_060181			osteoblast differentiation promoting factor						glycerol metabolic process|lipid metabolic process	cytoplasm|cytoskeleton|integral to membrane|plasma membrane	glycerophosphodiester phosphodiesterase activity|glycerophosphoinositol inositolphosphodiesterase activity|metal ion binding			ovary(2)	2	Renal(35;0.156)																	---	---	---	---
DLG3	1741	broad.mit.edu	37	X	69676602	69676604	+	Intron	DEL	TTT	-	-	rs71909380		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69676602_69676604delTTT	uc004dyi.1	+						DLG3_uc004dyj.1_Intron|DLG3_uc011mpn.1_Intron	NM_021120	NP_066943			synapse-associated protein 102 isoform a						axon guidance|negative regulation of cell proliferation|synaptic transmission	plasma membrane	guanylate kinase activity			large_intestine(1)|pancreas(1)	2	Renal(35;0.156)																	---	---	---	---
DLG3	1741	broad.mit.edu	37	X	69680003	69680003	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69680003delT	uc004dyi.1	+						DLG3_uc004dyj.1_Intron|DLG3_uc011mpn.1_Intron	NM_021120	NP_066943			synapse-associated protein 102 isoform a						axon guidance|negative regulation of cell proliferation|synaptic transmission	plasma membrane	guanylate kinase activity			large_intestine(1)|pancreas(1)	2	Renal(35;0.156)																	---	---	---	---
TEX11	56159	broad.mit.edu	37	X	69811475	69811475	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69811475delA	uc004dyl.2	-						TEX11_uc004dyk.2_Intron|TEX11_uc004dym.2_Intron	NM_001003811	NP_001003811			testis expressed sequence 11 isoform 1								protein binding			ovary(3)|breast(1)|skin(1)	5	Renal(35;0.156)																	---	---	---	---
ZMYM3	9203	broad.mit.edu	37	X	70469110	70469111	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70469110_70469111insA	uc004dzh.1	-						BCYRN1_uc011mpt.1_Intron|ZMYM3_uc004dzi.1_Intron|ZMYM3_uc004dzj.1_Intron|ZMYM3_uc011mpu.1_3'UTR|ZMYM3_uc004dzk.3_3'UTR|ZMYM3_uc004dzl.3_3'UTR|ZMYM3_uc004dzm.3_3'UTR	NM_201599	NP_963893			zinc finger protein 261						multicellular organismal development	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Renal(35;0.156)																	---	---	---	---
NONO	4841	broad.mit.edu	37	X	70518776	70518777	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70518776_70518777insT	uc004dzo.2	+						BCYRN1_uc011mpt.1_Intron|NONO_uc004dzn.2_Intron|NONO_uc004dzp.2_Intron|NONO_uc011mpv.1_Intron|NONO_uc004dzq.2_Intron|ITGB1BP2_uc004dzr.1_5'Flank|ITGB1BP2_uc004dzs.1_5'Flank	NM_001145408	NP_001138880			non-POU domain containing, octamer-binding						DNA recombination|DNA repair|mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|transcription, DNA-dependent	nuclear matrix|paraspeckles	DNA binding|identical protein binding|nucleotide binding|RNA binding		NONO/TFE3(2)	ovary(2)|kidney(2)	4	Renal(35;0.156)							T	TFE3	papillary renal cancer								---	---	---	---
TAF1	6872	broad.mit.edu	37	X	70683134	70683134	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70683134delT	uc004dzu.3	+						BCYRN1_uc011mpt.1_Intron|TAF1_uc004dzt.3_Intron|TAF1_uc004dzv.3_Intron|TAF1_uc010nle.1_Intron|TAF1_uc010nlf.1_Intron|TAF1_uc004dzx.2_Intron|TAF1_uc004dzy.2_Intron|TAF1_uc004dzw.1_Intron|TAF1_uc010nlg.1_Intron	NM_138923	NP_620278			TBP-associated factor 1 isoform 2						G1 phase of mitotic cell cycle|interspecies interaction between organisms|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription initiation from RNA polymerase II promoter|protein autophosphorylation|regulation of transcription involved in G2/M-phase of mitotic cell cycle|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	MLL1 complex|transcription factor TFIID complex	ATP binding|histone acetyl-lysine binding|histone acetyltransferase activity|p53 binding|protein binding|protein serine/threonine kinase activity|sequence-specific DNA binding|TBP-class protein binding|transcription coactivator activity			ovary(7)|breast(4)|large_intestine(2)|central_nervous_system(2)|lung(1)|skin(1)	17	Renal(35;0.156)	all_lung(315;0.000321)																---	---	---	---
OGT	8473	broad.mit.edu	37	X	70794604	70794609	+	3'UTR	DEL	TTTTTT	-	-	rs11345203		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70794604_70794609delTTTTTT	uc004eaa.1	+	22					BCYRN1_uc011mpt.1_Intron|OGT_uc004eab.1_3'UTR|OGT_uc004eac.2_3'UTR|OGT_uc004ead.2_3'UTR	NM_181672	NP_858058			O-linked GlcNAc transferase isoform 1						cellular response to retinoic acid|positive regulation of granulocyte differentiation|positive regulation of histone H3-K4 methylation|positive regulation of proteolysis|protein O-linked glycosylation|signal transduction	cytosol|MLL5-L complex	enzyme activator activity|protein binding|protein N-acetylglucosaminyltransferase activity			ovary(3)|kidney(1)|pancreas(1)	5	Renal(35;0.156)																	---	---	---	---
NHSL2	340527	broad.mit.edu	37	X	71207061	71207061	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71207061delA	uc011mqa.1	+							NM_001013627	NP_001013649			NHS-like 2												0	Renal(35;0.156)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	71504655	71504656	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71504655_71504656delTT								RPS4X (7514 upstream) : CITED1 (16834 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	71519452	71519452	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71519452delC								RPS4X (22311 upstream) : CITED1 (2038 downstream)																																			---	---	---	---
HDAC8	55869	broad.mit.edu	37	X	71577763	71577763	+	Intron	DEL	T	-	-	rs77541507		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71577763delT	uc004eau.2	-						HDAC8_uc011mqe.1_Intron|HDAC8_uc011mqf.1_Intron|HDAC8_uc011mqg.1_Intron	NM_018486	NP_060956			histone deacetylase 8						chromatin assembly or disassembly|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|nuclear chromosome	histone deacetylase activity (H3-K16 specific)|metal ion binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|transcription factor binding				0	Renal(35;0.156)				Vorinostat(DB02546)													---	---	---	---
HDAC8	55869	broad.mit.edu	37	X	71710648	71710648	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71710648delA	uc004eau.2	-						HDAC8_uc011mqe.1_Intron|HDAC8_uc011mqf.1_Intron|HDAC8_uc011mqg.1_Intron|HDAC8_uc011mqh.1_Intron|HDAC8_uc010nlk.1_Intron|HDAC8_uc004eav.2_Intron|HDAC8_uc004eaw.2_Intron	NM_018486	NP_060956			histone deacetylase 8						chromatin assembly or disassembly|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|nuclear chromosome	histone deacetylase activity (H3-K16 specific)|metal ion binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|transcription factor binding				0	Renal(35;0.156)				Vorinostat(DB02546)													---	---	---	---
Unknown	0	broad.mit.edu	37	X	72472256	72472256	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:72472256delT								NAP1L2 (37572 upstream) : CDX4 (194834 downstream)																																			---	---	---	---
CHIC1	53344	broad.mit.edu	37	X	72903158	72903158	+	3'UTR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:72903158delA	uc004ebk.3	+	6					CHIC1_uc010nlo.2_RNA|CHIC1_uc011mql.1_3'UTR|CHIC1_uc004ebl.3_3'UTR	NM_001039840	NP_001034929			cysteine-rich hydrophobic domain 1							cytoplasmic membrane-bounded vesicle|plasma membrane					0	Renal(35;0.156)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	73004887	73004888	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73004887_73004888delAA								CHIC1 (97952 upstream) : TSIX (7152 downstream)																																			---	---	---	---
XIST	7503	broad.mit.edu	37	X	73070114	73070114	+	RNA	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73070114delA	uc004ebm.1	-	1		c.2475delT				NR_001564				Homo sapiens cDNA: FLJ21545 fis, clone COL06195.												0																		---	---	---	---
NCRNA00183	554203	broad.mit.edu	37	X	73181463	73181464	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73181463_73181464delTT	uc004ebo.2	+						NCRNA00183_uc004ebp.2_Intron					Homo sapiens cDNA FLJ31610 fis, clone NT2RI2002865.												0																		---	---	---	---
NCRNA00183	554203	broad.mit.edu	37	X	73202545	73202545	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73202545delA	uc004ebo.2	+						NCRNA00183_uc004ebp.2_Intron					Homo sapiens cDNA FLJ31610 fis, clone NT2RI2002865.												0																		---	---	---	---
NCRNA00182	100302692	broad.mit.edu	37	X	73428598	73428598	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73428598delA	uc010nlq.1	-						uc004ebq.1_Intron					Homo sapiens cDNA FLJ33139 fis, clone UTERU1000109.												0																		---	---	---	---
NCRNA00182	100302692	broad.mit.edu	37	X	73441699	73441699	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73441699delA	uc010nlq.1	-						uc004ebq.1_Intron					Homo sapiens cDNA FLJ33139 fis, clone UTERU1000109.												0																		---	---	---	---
SLC16A2	6567	broad.mit.edu	37	X	73702539	73702539	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73702539delT	uc004ebt.2	+							NM_006517	NP_006508			solute carrier family 16, member 2							integral to plasma membrane|membrane fraction	monocarboxylic acid transmembrane transporter activity|symporter activity			breast(2)|ovary(1)	3					Pyruvic acid(DB00119)													---	---	---	---
Unknown	0	broad.mit.edu	37	X	73886320	73886320	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73886320delT								RLIM (51859 upstream) : KIAA2022 (66372 downstream)																																			---	---	---	---
KIAA2022	340533	broad.mit.edu	37	X	74071426	74071427	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:74071426_74071427delAA	uc004eby.2	-							NM_001008537	NP_001008537			hypothetical protein LOC340533						base-excision repair, gap-filling|DNA replication proofreading|DNA replication, removal of RNA primer|nucleotide-excision repair, DNA gap filling|regulation of mitotic cell cycle|S phase of mitotic cell cycle	delta DNA polymerase complex	3'-5'-exodeoxyribonuclease activity|DNA-directed DNA polymerase activity			ovary(7)|large_intestine(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	74153326	74153326	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:74153326delC								KIAA2022 (8039 upstream) : ABCB7 (119781 downstream)																																			---	---	---	---
UPRT	139596	broad.mit.edu	37	X	74499966	74499967	+	Intron	INS	-	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:74499966_74499967insG	uc004ecb.1	+						UPRT_uc010nlu.1_Intron|UPRT_uc004ecc.1_Intron|UPRT_uc004ecd.1_Intron|UPRT_uc004ece.1_Intron	NM_145052	NP_659489			uracil phosphoribosyltransferase (FUR1) homolog						nucleoside metabolic process	cytoplasm|nucleus					0																		---	---	---	---
ZDHHC15	158866	broad.mit.edu	37	X	74651360	74651360	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:74651360delA	uc004ecg.2	-						ZDHHC15_uc004ech.2_Intron|ZDHHC15_uc011mqo.1_Intron	NM_144969	NP_659406			zinc finger, DHHC-type containing 15 isoform 1							integral to membrane	zinc ion binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	75127170	75127170	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:75127170delT								MAGEE2 (122099 upstream) : CXorf26 (265601 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	75313505	75313505	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:75313505delT								MAGEE2 (308434 upstream) : CXorf26 (79266 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	77345261	77345261	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77345261delT								ATP7A (39370 upstream) : PGK1 (14405 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	77469251	77469251	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77469251delT								TAF9B (74072 upstream) : CYSLTR1 (58880 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	77499067	77499067	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77499067delA								TAF9B (103888 upstream) : CYSLTR1 (29064 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	78880436	78880437	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:78880436_78880437delTT								ITM2A (257389 upstream) : TBX22 (389818 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	79505589	79505589	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:79505589delT	uc004edk.1	-											Homo sapiens cDNA FLJ26841 fis, clone PRS07619.																														---	---	---	---
Unknown	0	broad.mit.edu	37	X	79750201	79750201	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:79750201delT								FAM46D (49391 upstream) : BRWD3 (181482 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	80084911	80084912	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:80084911_80084912delTC								BRWD3 (19678 upstream) : HMGN5 (284288 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	80160022	80160022	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:80160022delT								BRWD3 (94789 upstream) : HMGN5 (209178 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	80207344	80207344	+	IGR	DEL	A	-	-	rs111487931		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:80207344delA								BRWD3 (142111 upstream) : HMGN5 (161856 downstream)																																			---	---	---	---
HMGN5	79366	broad.mit.edu	37	X	80376944	80376944	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:80376944delA	uc004eee.1	-							NM_030763	NP_110390			high-mobility group nucleosome binding domain 5						chromatin modification|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin|nucleolus	chromatin binding|DNA binding			lung(1)	1																OREG0019884	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	X	80625568	80625569	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:80625568_80625569insT								SH3BGRL (71526 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	81278469	81278469	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:81278469delA								SH3BGRL (724427 upstream) : None (None downstream)																																			---	---	---	---
HDX	139324	broad.mit.edu	37	X	83608656	83608657	+	Intron	INS	-	AGAT	AGAT	rs142525193		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83608656_83608657insAGAT	uc004eek.1	-						HDX_uc011mqv.1_Intron|HDX_uc004eel.1_Intron	NM_144657	NP_653258			highly divergent homeobox							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
HDX	139324	broad.mit.edu	37	X	83668637	83668637	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83668637delT	uc004eek.1	-						HDX_uc011mqv.1_Intron|HDX_uc004eel.1_Intron	NM_144657	NP_653258			highly divergent homeobox							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
HDX	139324	broad.mit.edu	37	X	83731553	83731556	+	Intron	DEL	AAAA	-	-	rs67000756		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83731553_83731556delAAAA	uc004eek.1	-						HDX_uc011mqv.1_Intron|HDX_uc004eel.1_Intron	NM_144657	NP_653258			highly divergent homeobox							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	84099753	84099753	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84099753delC								HDX (342295 upstream) : UBE2DNL (89404 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	84142246	84142247	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84142246_84142247delAA								HDX (384788 upstream) : UBE2DNL (46910 downstream)																																			---	---	---	---
APOOL	139322	broad.mit.edu	37	X	84309334	84309335	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84309334_84309335insT	uc004eem.2	+						APOOL_uc010nmp.2_Intron	NM_198450	NP_940852			apolipoprotein O-like precursor							extracellular region					0																		---	---	---	---
CHM	1121	broad.mit.edu	37	X	85274991	85274992	+	Intron	INS	-	A	A	rs11409659		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:85274991_85274992insA	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	85629310	85629310	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:85629310delA	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	86623916	86623917	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:86623916_86623917delTT								DACH2 (536311 upstream) : KLHL4 (148798 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	88133210	88133211	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:88133210_88133211insA								CPXCR1 (123427 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	88526111	88526111	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:88526111delA								CPXCR1 (516328 upstream) : TGIF2LX (650829 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	89459155	89459155	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:89459155delT								TGIF2LX (281275 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	89763767	89763767	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:89763767delA								TGIF2LX (585887 upstream) : PABPC5 (925830 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	90881001	90881002	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:90881001_90881002delTT								PABPC5 (187419 upstream) : PCDH11X (153302 downstream)																																			---	---	---	---
PCDH11X	27328	broad.mit.edu	37	X	91415156	91415156	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:91415156delT	uc004efk.1	+						PCDH11X_uc004efl.1_Intron|PCDH11X_uc004efo.1_Intron|PCDH11X_uc010nmv.1_Intron|PCDH11X_uc004efm.1_Intron|PCDH11X_uc004efn.1_Intron	NM_032968	NP_116750			protocadherin 11 X-linked isoform c						homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2																		---	---	---	---
PCDH11X	27328	broad.mit.edu	37	X	91497962	91497962	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:91497962delT	uc004efk.1	+						PCDH11X_uc004efl.1_Intron|PCDH11X_uc004efo.1_Intron|PCDH11X_uc010nmv.1_Intron|PCDH11X_uc004efm.1_Intron|PCDH11X_uc004efn.1_Intron	NM_032968	NP_116750			protocadherin 11 X-linked isoform c						homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	92869294	92869295	+	IGR	DEL	CA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:92869294_92869295delCA								PCDH11X (991068 upstream) : NAP1L3 (56634 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	93085262	93085262	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:93085262delT								FAM133A (118001 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	94168970	94168970	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:94168970delA								None (None upstream) : MIR548M (149170 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	94784929	94784929	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:94784929delA								MIR548M (466704 upstream) : LOC643486 (807157 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	95032236	95032236	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:95032236delT								MIR548M (714011 upstream) : LOC643486 (559850 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	95304123	95304123	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:95304123delA								MIR548M (985898 upstream) : LOC643486 (287963 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	95325076	95325076	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:95325076delA								None (None upstream) : LOC643486 (267010 downstream)																																			---	---	---	---
RPA4	29935	broad.mit.edu	37	X	96140184	96140185	+	3'UTR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:96140184_96140185delAA	uc004efv.3	+	1					DIAPH2_uc004eft.3_Intron|DIAPH2_uc004efu.3_Intron|DIAPH2_uc004efs.2_Intron	NM_013347	NP_037479			replication protein A4, 34kDa						DNA damage checkpoint|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair	DNA replication factor A complex|nucleoplasm	single-stranded DNA binding				0													Other_identified_genes_with_known_or_suspected_DNA_repair_function					---	---	---	---
DIAPH2	1730	broad.mit.edu	37	X	96547195	96547195	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:96547195delT	uc004efu.3	+						DIAPH2_uc004eft.3_Intron	NM_006729	NP_006720			diaphanous 2 isoform 156						cell differentiation|cytokinesis|multicellular organismal development|oogenesis	cytosol|early endosome|Golgi apparatus|mitochondrion|nucleolus	receptor binding|Rho GTPase binding			ovary(3)|lung(1)	4																		---	---	---	---
DIAPH2	1730	broad.mit.edu	37	X	96624848	96624848	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:96624848delA	uc004efu.3	+						DIAPH2_uc004eft.3_Intron	NM_006729	NP_006720			diaphanous 2 isoform 156						cell differentiation|cytokinesis|multicellular organismal development|oogenesis	cytosol|early endosome|Golgi apparatus|mitochondrion|nucleolus	receptor binding|Rho GTPase binding			ovary(3)|lung(1)	4																		---	---	---	---
DIAPH2	1730	broad.mit.edu	37	X	96672830	96672831	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:96672830_96672831delTT	uc004efu.3	+						DIAPH2_uc004eft.3_Intron	NM_006729	NP_006720			diaphanous 2 isoform 156						cell differentiation|cytokinesis|multicellular organismal development|oogenesis	cytosol|early endosome|Golgi apparatus|mitochondrion|nucleolus	receptor binding|Rho GTPase binding			ovary(3)|lung(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	96906512	96906512	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:96906512delT								DIAPH2 (50916 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	99788386	99788386	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99788386delT								PCDH19 (123115 upstream) : TNMD (51404 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	99861151	99861152	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99861151_99861152insT								TNMD (6269 upstream) : TSPAN6 (22643 downstream)																																			---	---	---	---
SRPX2	27286	broad.mit.edu	37	X	99897035	99897035	+	5'Flank	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99897035delG	uc004egb.2	+							NM_014467	NP_055282			sushi-repeat-containing protein, X-linked 2						angiogenesis|cell motility|cell-cell adhesion|positive regulation of cell migration involved in sprouting angiogenesis|regulation of phosphorylation	cytoplasm|extracellular region	receptor binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	100070848	100070849	+	IGR	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100070848_100070849insA								SYTL4 (83717 upstream) : CSTF2 (4499 downstream)																																			---	---	---	---
TMEM35	59353	broad.mit.edu	37	X	100339898	100339898	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100339898delA	uc004egw.2	+							NM_021637	NP_067650			transmembrane protein 35							cytoplasmic membrane-bounded vesicle|integral to membrane|peroxisomal membrane					0																		---	---	---	---
CENPI	2491	broad.mit.edu	37	X	100363352	100363352	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100363352delT	uc004egx.2	+						CENPI_uc011mrg.1_Intron|CENPI_uc004egy.2_Intron	NM_006733	NP_006724			centromere protein I						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	cytosol|kinetochore|nucleoplasm	protein binding			skin(1)	1																		---	---	---	---
DRP2	1821	broad.mit.edu	37	X	100486614	100486614	+	5'UTR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100486614delC	uc004egz.2	+	3					DRP2_uc011mrh.1_Intron	NM_001939	NP_001930			dystrophin related protein 2						central nervous system development	cytoplasm|cytoskeleton	zinc ion binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	100846960	100846960	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100846960delT								ARMCX1 (37287 upstream) : ARMCX6 (23154 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	100860001	100860001	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100860001delT								ARMCX1 (50328 upstream) : ARMCX6 (10113 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	101130411	101130411	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101130411delG								NXF5 (17862 upstream) : ZMAT1 (6852 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	101211915	101211915	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101211915delT								ZMAT1 (24915 upstream) : TCEAL2 (168745 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	101219205	101219205	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101219205delA								ZMAT1 (32205 upstream) : TCEAL2 (161455 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	102355894	102355894	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102355894delT								NXF3 (7872 upstream) : BEX4 (114126 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	102524024	102524024	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102524024delT								TCEAL8 (13903 upstream) : TCEAL5 (4595 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	102706294	102706295	+	IGR	INS	-	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102706294_102706295insC								NGFRAP1 (73295 upstream) : RAB40A (48387 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	103025684	103025686	+	IGR	DEL	AAA	-	-	rs112451093		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:103025684_103025686delAAA								GLRA4 (42132 upstream) : PLP1 (5753 downstream)																																			---	---	---	---
IL1RAPL2	26280	broad.mit.edu	37	X	104195397	104195398	+	Intron	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:104195397_104195398delTT	uc004elz.1	+							NM_017416	NP_059112			interleukin 1 receptor accessory protein-like 2						central nervous system development|innate immune response	integral to membrane	interleukin-1, Type II, blocking receptor activity			breast(2)|ovary(1)	3																		---	---	---	---
IL1RAPL2	26280	broad.mit.edu	37	X	104365599	104365599	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:104365599delT	uc004elz.1	+							NM_017416	NP_059112			interleukin 1 receptor accessory protein-like 2						central nervous system development|innate immune response	integral to membrane	interleukin-1, Type II, blocking receptor activity			breast(2)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	105355174	105355174	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105355174delA								SERPINA7 (72458 upstream) : MUM1L1 (57124 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	105718713	105718713	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105718713delA								MUM1L1 (265765 upstream) : CXorf57 (136447 downstream)																																			---	---	---	---
MORC4	79710	broad.mit.edu	37	X	106136471	106136472	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106136471_106136472delAA	uc004emp.3	-											SubName: Full=cDNA FLJ59044, highly similar to LINE-1 reverse transcriptase homolog;								ATP binding|zinc ion binding			ovary(1)	1																		---	---	---	---
MORC4	79710	broad.mit.edu	37	X	106147804	106147805	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106147804_106147805insA	uc004emp.3	-						CLDN2_uc004emq.1_Intron|RIPPLY1_uc004emr.1_5'Flank|RIPPLY1_uc004ems.1_5'Flank					SubName: Full=cDNA FLJ59044, highly similar to LINE-1 reverse transcriptase homolog;								ATP binding|zinc ion binding			ovary(1)	1																		---	---	---	---
MORC4	79710	broad.mit.edu	37	X	106228910	106228913	+	Intron	DEL	AAAA	-	-	rs112124198		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106228910_106228913delAAAA	uc004emu.3	-						MORC4_uc004emp.3_Intron|MORC4_uc004emv.3_Intron|MORC4_uc004emw.3_Intron	NM_024657	NP_078933			zinc finger, CW type with coiled-coil domain 2								ATP binding|zinc ion binding			ovary(1)	1																		---	---	---	---
CXorf41	139212	broad.mit.edu	37	X	106461964	106461964	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106461964delA	uc004enc.2	+						CXorf41_uc004end.2_Intron	NM_173494	NP_775765			hypothetical protein LOC139212												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	106547681	106547681	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106547681delA								CXorf41 (60209 upstream) : PRPS1 (323973 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	106822569	106822569	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106822569delA								CXorf41 (335097 upstream) : PRPS1 (49085 downstream)																																			---	---	---	---
MID2	11043	broad.mit.edu	37	X	107082345	107082346	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107082345_107082346delAA	uc004enl.2	+						MID2_uc004enk.2_Intron	NM_012216	NP_036348			midline 2 isoform 1							centrosome|microtubule	ligase activity|zinc ion binding			ovary(1)	1																		---	---	---	---
VSIG1	340547	broad.mit.edu	37	X	107286140	107286140	+	5'Flank	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107286140delT	uc004eno.2	+						VSIG1_uc011msk.1_5'Flank	NM_182607	NP_872413			V-set and immunoglobulin domain containing 1							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
ATG4A	115201	broad.mit.edu	37	X	107355626	107355626	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107355626delT	uc004enr.2	+						ATG4A_uc004ent.2_Intron|ATG4A_uc004ens.2_Intron|ATG4A_uc011msl.1_Intron|ATG4A_uc010npi.2_Intron	NM_052936	NP_443168			autophagy-related cysteine endopeptidase 2						autophagy|protein transport|proteolysis	cytoplasm	cysteine-type peptidase activity			pancreas(1)	1																		---	---	---	---
ATG4A	115201	broad.mit.edu	37	X	107396439	107396439	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107396439delA	uc004enr.2	+						ATG4A_uc004ent.2_Intron|ATG4A_uc004ens.2_Intron|ATG4A_uc011msl.1_Intron|ATG4A_uc010npi.2_Intron|ATG4A_uc004enu.2_Intron|COL4A6_uc011msm.1_Intron	NM_052936	NP_443168			autophagy-related cysteine endopeptidase 2						autophagy|protein transport|proteolysis	cytoplasm	cysteine-type peptidase activity			pancreas(1)	1																		---	---	---	---
COL4A6	1288	broad.mit.edu	37	X	107681288	107681288	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107681288delC	uc004enw.3	-						COL4A6_uc004env.3_Intron|COL4A6_uc011msn.1_Intron|COL4A6_uc010npk.2_Intron|COL4A6_uc004enx.2_Intron|COL4A6_uc004eny.2_Intron|COL4A5_uc004enz.1_5'Flank|COL4A5_uc011mso.1_5'Flank	NM_001847	NP_001838			type IV alpha 6 collagen isoform A precursor						cell adhesion|extracellular matrix organization	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(6)|urinary_tract(1)|large_intestine(1)	8														Alport_syndrome_with_Diffuse_Leiomyomatosis				---	---	---	---
Unknown	0	broad.mit.edu	37	X	108196856	108196856	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:108196856delT								IRS4 (217249 upstream) : GUCY2F (419280 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	108260722	108260722	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:108260722delG								IRS4 (281115 upstream) : GUCY2F (355414 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	108761750	108761750	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:108761750delA								GUCY2F (36465 upstream) : NXT2 (17260 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	108801091	108801091	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:108801091delA								NXT2 (13178 upstream) : KCNE1L (65840 downstream)																																			---	---	---	---
AMMECR1	9949	broad.mit.edu	37	X	109578129	109578129	+	Intron	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:109578129delG	uc004eoq.2	-							NM_015365	NP_056180			AMMECR1 protein isoform 1												0																		---	---	---	---
TDGF3	6998	broad.mit.edu	37	X	109762856	109762863	+	5'Flank	DEL	TTTTTTTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:109762856_109762863delTTTTTTTT	uc004eos.1	+							NR_002718				Human (clone CR-3) teratocarcinoma-derived growth factor 3 (TDGF3) mRNA, complete cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	109776904	109776904	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:109776904delA								TDGF3 (10655 upstream) : CHRDL1 (140181 downstream)																																			---	---	---	---
PAK3	5063	broad.mit.edu	37	X	110370672	110370673	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110370672_110370673delAA	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|uc004epb.2_RNA	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)			---	---	---	---
CAPN6	827	broad.mit.edu	37	X	110493956	110493956	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110493956delA	uc004epc.1	-						CAPN6_uc011msu.1_Intron	NM_014289	NP_055104			calpain 6						microtubule bundle formation|proteolysis|regulation of cytoskeleton organization	perinuclear region of cytoplasm|spindle microtubule	calcium-dependent cysteine-type endopeptidase activity|microtubule binding			ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|skin(1)	6																		---	---	---	---
TRPC5	7224	broad.mit.edu	37	X	111119264	111119265	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:111119264_111119265delAA	uc004epl.1	-						TRPC5_uc004epm.1_Intron	NM_012471	NP_036603			transient receptor potential cation channel,						axon guidance	calcium channel complex|integral to plasma membrane	protein binding|store-operated calcium channel activity			urinary_tract(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	112126233	112126233	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:112126233delT								AMOT (42190 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	112490735	112490735	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:112490735delT								AMOT (406692 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	112706248	112706248	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:112706248delA								AMOT (622205 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	113022946	113022946	+	IGR	DEL	A	-	-	rs11309345		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:113022946delA								AMOT (938903 upstream) : HTR2C (795605 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	114666396	114666396	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114666396delT								LUZP4 (124277 upstream) : PLS3 (128810 downstream)																																			---	---	---	---
PLS3	5358	broad.mit.edu	37	X	114834254	114834254	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114834254delT	uc004eqd.2	+						PLS3_uc010nqf.2_Intron|PLS3_uc010nqg.2_Intron|PLS3_uc011mtf.1_Intron|PLS3_uc004eqe.2_Intron|PLS3_uc011mtg.1_Intron|PLS3_uc011mth.1_Intron	NM_005032	NP_005023			plastin 3							cytoplasm	actin binding|calcium ion binding			lung(1)|breast(1)	2																		---	---	---	---
PLS3	5358	broad.mit.edu	37	X	114868272	114868272	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114868272delT	uc004eqd.2	+						PLS3_uc010nqg.2_Intron|PLS3_uc011mtf.1_Intron|PLS3_uc004eqe.2_Intron|PLS3_uc011mtg.1_Intron|PLS3_uc011mth.1_Intron	NM_005032	NP_005023			plastin 3							cytoplasm	actin binding|calcium ion binding			lung(1)|breast(1)	2																		---	---	---	---
PLS3	5358	broad.mit.edu	37	X	114881754	114881754	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114881754delA	uc004eqd.2	+						PLS3_uc011mtf.1_Intron|PLS3_uc004eqe.2_Intron|PLS3_uc011mtg.1_Intron|PLS3_uc011mth.1_Intron|PLS3_uc011mti.1_Intron|PLS3_uc011mtj.1_Intron|PLS3_uc011mtk.1_Intron|PLS3_uc011mtl.1_Intron	NM_005032	NP_005023			plastin 3							cytoplasm	actin binding|calcium ion binding			lung(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	115239854	115239855	+	IGR	INS	-	CTTCTT	CTTCTT			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:115239854_115239855insCTTCTT								PLS3 (354864 upstream) : AGTR2 (62103 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	115239904	115239906	+	IGR	DEL	CTT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:115239904_115239906delCTT								PLS3 (354914 upstream) : AGTR2 (62052 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	115488486	115488486	+	IGR	DEL	T	-	-	rs66824101		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:115488486delT								AGTR2 (182263 upstream) : SLC6A14 (79288 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	116112141	116112142	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:116112141_116112142delAA								CXorf61 (518004 upstream) : KLHL13 (919635 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	116760682	116760683	+	IGR	DEL	AA	-	-	rs113578341		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:116760682_116760683delAA								None (None upstream) : KLHL13 (271094 downstream)																																			---	---	---	---
WDR44	54521	broad.mit.edu	37	X	117491684	117491684	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117491684delT	uc004eqn.2	+						WDR44_uc004eqo.2_Intron|WDR44_uc011mtr.1_Intron	NM_019045	NP_061918			WD repeat domain 44 protein							cytosol|endosome membrane|Golgi apparatus|perinuclear region of cytoplasm				lung(2)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	5																		---	---	---	---
WDR44	54521	broad.mit.edu	37	X	117532869	117532869	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117532869delA	uc004eqn.2	+						WDR44_uc004eqo.2_Intron|WDR44_uc011mtr.1_Intron|WDR44_uc010nqi.2_Intron	NM_019045	NP_061918			WD repeat domain 44 protein							cytosol|endosome membrane|Golgi apparatus|perinuclear region of cytoplasm				lung(2)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	5																		---	---	---	---
DOCK11	139818	broad.mit.edu	37	X	117733260	117733260	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117733260delA	uc004eqp.2	+						DOCK11_uc004eqq.2_Intron	NM_144658	NP_653259			dedicator of cytokinesis 11						blood coagulation	cytosol	GTP binding			ovary(3)	3																		---	---	---	---
DOCK11	139818	broad.mit.edu	37	X	117739055	117739055	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117739055delC	uc004eqp.2	+						DOCK11_uc004eqq.2_Intron	NM_144658	NP_653259			dedicator of cytokinesis 11						blood coagulation	cytosol	GTP binding			ovary(3)	3																		---	---	---	---
LONRF3	79836	broad.mit.edu	37	X	118120810	118120810	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118120810delT	uc004eqw.2	+						LONRF3_uc004eqx.2_Intron|LONRF3_uc004eqy.2_Intron|LONRF3_uc004eqz.2_Intron	NM_001031855	NP_001027026			LON peptidase N-terminal domain and ring finger						proteolysis		ATP-dependent peptidase activity|protein binding|zinc ion binding			breast(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	118295878	118295878	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118295878delT								KIAA1210 (11336 upstream) : PGRMC1 (74333 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	118360217	118360228	+	IGR	DEL	GTGTGTGTGTGT	-	-	rs72429094		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118360217_118360228delGTGTGTGTGTGT								KIAA1210 (75675 upstream) : PGRMC1 (9983 downstream)																																			---	---	---	---
NKRF	55922	broad.mit.edu	37	X	118741828	118741828	+	5'Flank	DEL	A	-	-	rs75105383		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118741828delA	uc004err.2	-							NM_017544	NP_060014			transcription factor NRF						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|double-stranded RNA binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	118914329	118914329	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118914329delT								ANKRD58 (20165 upstream) : RPL39 (6140 downstream)																																			---	---	---	---
AKAP14	158798	broad.mit.edu	37	X	119049475	119049475	+	Intron	DEL	T	-	-	rs150637958		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119049475delT	uc004ese.2	+						AKAP14_uc004esf.2_Intron	NM_178813	NP_848928			A kinase (PRKA) anchor protein 14 isoform a							cytoplasm					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	119083224	119083227	+	IGR	DEL	TAAC	-	-	rs72062566		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119083224_119083227delTAAC								NKAP (5489 upstream) : RHOXF2B (123014 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	119345949	119345949	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119345949delT								RHOXF1 (96102 upstream) : CXorf42 (24362 downstream)																																			---	---	---	---
FAM70A	55026	broad.mit.edu	37	X	119401448	119401448	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119401448delT	uc004eso.3	-						FAM70A_uc004esp.3_Intron|FAM70A_uc010nqo.2_Intron	NM_017938	NP_060408			hypothetical protein LOC55026 isoform 1							integral to membrane				lung(1)|breast(1)	2																		---	---	---	---
CUL4B	8450	broad.mit.edu	37	X	119680263	119680264	+	Intron	INS	-	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119680263_119680264insA	uc004esw.2	-						CUL4B_uc010nqq.2_Intron|CUL4B_uc004esv.2_Intron	NM_003588	NP_003579			cullin 4B isoform 1						cell cycle|DNA repair|ubiquitin-dependent protein catabolic process	Cul4B-RING ubiquitin ligase complex|nucleus	protein binding|ubiquitin protein ligase binding			lung(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	120160018	120160024	+	IGR	DEL	TTTTTTT	-	-	rs66871433		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:120160018_120160024delTTTTTTT								CT47A6 (64681 upstream) : GLUD2 (21438 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	120224002	120224002	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:120224002delT								GLUD2 (40208 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	121405572	121405572	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:121405572delT								None (None upstream) : GRIA3 (912524 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	121819637	121819637	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:121819637delA								None (None upstream) : GRIA3 (498459 downstream)																																			---	---	---	---
GRIA3	2892	broad.mit.edu	37	X	122374664	122374664	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:122374664delT	uc004etq.3	+						GRIA3_uc004etr.3_Intron|GRIA3_uc004ets.3_Intron|GRIA3_uc011muf.1_Intron	NM_007325	NP_015564			glutamate receptor, ionotrophic, AMPA 3 isoform						glutamate signaling pathway|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5					L-Glutamic Acid(DB00142)													---	---	---	---
GRIA3	2892	broad.mit.edu	37	X	122602138	122602138	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:122602138delA	uc004etq.3	+						GRIA3_uc004etr.3_Intron|GRIA3_uc004ets.3_Intron	NM_007325	NP_015564			glutamate receptor, ionotrophic, AMPA 3 isoform						glutamate signaling pathway|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5					L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	X	123054330	123054330	+	IGR	DEL	A	-	-	rs150233542		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123054330delA								XIAP (6509 upstream) : STAG2 (40145 downstream)																																			---	---	---	---
STAG2	10735	broad.mit.edu	37	X	123140956	123140957	+	Intron	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123140956_123140957delTC	uc004etz.3	+						STAG2_uc004eua.2_Intron|STAG2_uc004eub.2_Intron|STAG2_uc004euc.2_Intron|STAG2_uc004eud.2_Intron|STAG2_uc004eue.2_Intron	NM_006603	NP_006594			stromal antigen 2 isoform b						cell division|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|negative regulation of DNA endoreduplication|sister chromatid cohesion	chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(4)|skin(1)	5																		---	---	---	---
ODZ1	10178	broad.mit.edu	37	X	123599566	123599566	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123599566delT	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	124799598	124799599	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:124799598_124799599delAA								ODZ1 (701932 upstream) : DCAF12L2 (498915 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	126651928	126651929	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:126651928_126651929insT								CXorf64 (696162 upstream) : ACTRT1 (533014 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	128363480	128363480	+	IGR	DEL	A	-	-	rs56130950	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128363480delA								None (None upstream) : SMARCA1 (217000 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	129081269	129081269	+	IGR	DEL	A	-	-	rs56036907	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129081269delA								UTP14A (17542 upstream) : BCORL1 (35400 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	129097491	129097491	+	IGR	DEL	A	-	-	rs113253559		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129097491delA								UTP14A (33764 upstream) : BCORL1 (19178 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	129665894	129665895	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129665894_129665895insT								FAM45B (35162 upstream) : ENOX2 (91464 downstream)																																			---	---	---	---
ARHGAP36	158763	broad.mit.edu	37	X	130206252	130206252	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130206252delA	uc004evz.2	+						ARHGAP36_uc004ewa.2_Intron	NM_144967	NP_659404			hypothetical protein LOC158763 precursor						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	130226846	130226846	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130226846delT								ARHGAP36 (2990 upstream) : IGSF1 (180637 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	131037396	131037397	+	IGR	DEL	AC	-	-	rs72188053		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:131037396_131037397delAC								LOC286467 (72725 upstream) : MST4 (119848 downstream)																																			---	---	---	---
GPC3	2719	broad.mit.edu	37	X	132730014	132730014	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132730014delT	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	133446932	133446932	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133446932delT								CCDC160 (67126 upstream) : PHF6 (60410 downstream)																																			---	---	---	---
FAM122C	159091	broad.mit.edu	37	X	133944728	133944728	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133944728delT	uc004exz.1	+						FAM122C_uc010nru.1_Intron|FAM122C_uc004exw.2_Intron|FAM122C_uc004exx.2_Intron|FAM122C_uc011mvq.1_Intron|FAM122C_uc004exy.1_Intron	NM_138819	NP_620174			hypothetical protein LOC159091												0	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	134598462	134598462	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134598462delT								NCRNA00086 (38238 upstream) : DDX26B (56093 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	134614318	134614318	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134614318delT								NCRNA00086 (54094 upstream) : DDX26B (40237 downstream)																																			---	---	---	---
GPR112	139378	broad.mit.edu	37	X	135472142	135472142	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135472142delT	uc004ezu.1	+						GPR112_uc010nsb.1_Intron	NM_153834	NP_722576			G-protein coupled receptor 112						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(5)|large_intestine(2)|skin(2)|lung(1)|breast(1)|pancreas(1)	12	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
GPR112	139378	broad.mit.edu	37	X	135482406	135482406	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135482406delT	uc004ezu.1	+						GPR112_uc010nsb.1_Intron	NM_153834	NP_722576			G-protein coupled receptor 112						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(5)|large_intestine(2)|skin(2)|lung(1)|breast(1)|pancreas(1)	12	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
BRS3	680	broad.mit.edu	37	X	135574046	135574046	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135574046delT	uc004ezv.1	+							NM_001727	NP_001718			bombesin-like receptor 3						adult feeding behavior|glucose metabolic process|regulation of blood pressure	integral to membrane|plasma membrane	bombesin receptor activity			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	136356802	136356802	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:136356802delT								GPR101 (242969 upstream) : ZIC3 (291544 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	137669924	137669925	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:137669924_137669925delTT								None (None upstream) : LOC158696 (26967 downstream)																																			---	---	---	---
FGF13	2258	broad.mit.edu	37	X	137960304	137960304	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:137960304delT	uc004faq.2	-						FGF13_uc004far.2_Intron|FGF13_uc011mwj.1_Intron|FGF13_uc011mwk.1_Intron	NM_001139502	NP_001132974			fibroblast growth factor 13 isoform 3						cell-cell signaling|MAPKKK cascade|nervous system development	cytoplasm|nucleus	growth factor activity|protein kinase activator activity			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
FGF13	2258	broad.mit.edu	37	X	138101963	138101963	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138101963delA	uc004faq.2	-						FGF13_uc004far.2_Intron|FGF13_uc011mwj.1_Intron|FGF13_uc011mwk.1_Intron	NM_001139502	NP_001132974			fibroblast growth factor 13 isoform 3						cell-cell signaling|MAPKKK cascade|nervous system development	cytoplasm|nucleus	growth factor activity|protein kinase activator activity			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
MCF2	4168	broad.mit.edu	37	X	138708237	138708237	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138708237delT	uc004fau.2	-						MCF2_uc004fav.2_Intron|MCF2_uc011mwl.1_Intron|MCF2_uc010nsh.1_Intron|MCF2_uc011mwm.1_Intron|MCF2_uc011mwn.1_Intron|MCF2_uc004faw.2_Intron|MCF2_uc011mwo.1_Intron	NM_005369	NP_005360			MCF.2 cell line derived transforming sequence						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytoskeleton|cytosol|membrane|membrane fraction	protein binding|Rho guanyl-nucleotide exchange factor activity			lung(1)|pleura(1)	2	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	139189938	139189938	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:139189938delT								CXorf66 (142261 upstream) : SOX3 (395214 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	139674058	139674059	+	IGR	DEL	TT	-	-	rs112357872		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:139674058_139674059delTT								SOX3 (86833 upstream) : RP1-177G6.2 (117873 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	139883352	139883353	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:139883352_139883353delTT								CDR1 (16629 upstream) : MIR320D2 (124984 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	142068004	142068005	+	IGR	DEL	TC	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:142068004_142068005delTC								MAGEC2 (774928 upstream) : SPANXN4 (45699 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	142318824	142318825	+	IGR	INS	-	GT	GT	rs34942744		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:142318824_142318825insGT								SPANXN4 (196759 upstream) : SPANXN3 (277740 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	142507988	142507989	+	IGR	DEL	TT	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:142507988_142507989delTT								SPANXN4 (385923 upstream) : SPANXN3 (88576 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	143365805	143365806	+	IGR	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:143365805_143365806insT								UBE2NL (397450 upstream) : SPANXN1 (963301 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	143954097	143954097	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:143954097delT								UBE2NL (985742 upstream) : SPANXN1 (375010 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	144461251	144461251	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:144461251delT								SPANXN1 (123523 upstream) : SLITRK2 (438096 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	144919869	144919869	+	IGR	DEL	G	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:144919869delG								CXorf1 (8501 upstream) : MIR890 (155924 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	145462208	145462208	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:145462208delA								MIR891A (352818 upstream) : CXorf51 (429094 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	146032857	146032857	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:146032857delA								CXorf51 (140933 upstream) : MIR513C (238365 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	146306738	146306738	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:146306738delA								MIR513A1 (11629 upstream) : MIR513A2 (606 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	146882864	146882864	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:146882864delA								MIR514-3 (516618 upstream) : ASFMR1 (108085 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	146886491	146886491	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:146886491delA								MIR514-3 (520245 upstream) : ASFMR1 (104458 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	147299666	147299666	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147299666delA								FMR1NB (191486 upstream) : AFF2 (282473 downstream)																																			---	---	---	---
AFF2	2334	broad.mit.edu	37	X	147592773	147592774	+	Intron	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147592773_147592774delAA	uc004fcp.2	+						AFF2_uc004fco.2_Intron|AFF2_uc004fcq.2_Intron|AFF2_uc004fcr.2_Intron|AFF2_uc011mxb.1_Intron|AFF2_uc004fcs.2_Intron	NM_002025	NP_002016			fragile X mental retardation 2						brain development|mRNA processing|regulation of RNA splicing|RNA splicing	nuclear speck	G-quadruplex RNA binding|protein binding			ovary(3)|pancreas(2)	5	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
AFF2	2334	broad.mit.edu	37	X	147969553	147969554	+	Intron	INS	-	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147969553_147969554insT	uc004fcp.2	+						AFF2_uc004fco.2_Intron|AFF2_uc004fcq.2_Intron|AFF2_uc004fcr.2_Intron|AFF2_uc011mxb.1_Intron|AFF2_uc004fcs.2_Intron|AFF2_uc011mxc.1_Intron	NM_002025	NP_002016			fragile X mental retardation 2						brain development|mRNA processing|regulation of RNA splicing|RNA splicing	nuclear speck	G-quadruplex RNA binding|protein binding			ovary(3)|pancreas(2)	5	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	149030147	149030147	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149030147delT								MAGEA8 (15539 upstream) : CXorf40B (67576 downstream)																																			---	---	---	---
MAMLD1	10046	broad.mit.edu	37	X	149575659	149575659	+	Intron	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149575659delA	uc011mxu.1	+						MAMLD1_uc011mxt.1_Intron					RecName: Full=Mastermind-like domain-containing protein 1;          Short=Protein CG1; AltName: Full=F18;						male gonad development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
MAMLD1	10046	broad.mit.edu	37	X	149584318	149584318	+	Intron	DEL	T	-	-	rs111568549		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149584318delT	uc011mxu.1	+						MAMLD1_uc011mxt.1_Intron					RecName: Full=Mastermind-like domain-containing protein 1;          Short=Protein CG1; AltName: Full=F18;						male gonad development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	149686108	149686108	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149686108delT								MAMLD1 (3662 upstream) : MTM1 (50939 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	150604145	150604145	+	IGR	DEL	A	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150604145delA								VMA21 (26310 upstream) : PASD1 (127862 downstream)																																			---	---	---	---
GABRA3	2556	broad.mit.edu	37	X	151393603	151393603	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151393603delC	uc010ntk.1	-							NM_000808	NP_000799			gamma-aminobutyric acid A receptor, alpha 3						gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity|protein binding			ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)				Alprazolam(DB00404)|Diazepam(DB00829)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)													---	---	---	---
Unknown	0	broad.mit.edu	37	X	151660370	151660370	+	IGR	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151660370delT								GABRA3 (40539 upstream) : GABRQ (146267 downstream)																																			---	---	---	---
ZNF185	7739	broad.mit.edu	37	X	152087880	152087882	+	Intron	DEL	CCT	-	-	rs72085496		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152087880_152087882delCCT	uc010ntv.1	+						ZNF185_uc011myg.1_Intron|ZNF185_uc011myh.1_Intron|ZNF185_uc011myi.1_Intron|ZNF185_uc011myj.1_Intron|ZNF185_uc011myk.1_Intron|ZNF185_uc004fgw.3_Intron|ZNF185_uc004fgu.2_Intron|ZNF185_uc004fgv.2_5'Flank	NM_007150	NP_009081			zinc finger protein 185							cytoplasm|cytoskeleton|focal adhesion	zinc ion binding			ovary(3)	3	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
ZNF185	7739	broad.mit.edu	37	X	152101166	152101166	+	Intron	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152101166delC	uc010ntv.1	+						ZNF185_uc011myg.1_Intron|ZNF185_uc011myh.1_Intron|ZNF185_uc011myi.1_Intron|ZNF185_uc011myj.1_Intron|ZNF185_uc011myk.1_Intron|ZNF185_uc004fgw.3_Intron|ZNF185_uc004fgu.2_Intron|ZNF185_uc004fgv.2_Intron	NM_007150	NP_009081			zinc finger protein 185							cytoplasm|cytoskeleton|focal adhesion	zinc ion binding			ovary(3)	3	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
PNMA5	114824	broad.mit.edu	37	X	152166129	152166129	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152166129delT	uc004fha.3	-							NM_052926	NP_443158			paraneoplastic antigen like 5						apoptosis					ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
PNMA5	114824	broad.mit.edu	37	X	152196637	152196638	+	Intron	DEL	GA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152196637_152196638delGA	uc004fha.3	-							NM_052926	NP_443158			paraneoplastic antigen like 5						apoptosis					ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
SRPK3	26576	broad.mit.edu	37	X	153048649	153048649	+	Intron	DEL	C	-	-	rs72481508		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153048649delC	uc004fil.2	+						SRPK3_uc004fik.2_Intron|SRPK3_uc010nul.2_Intron|SRPK3_uc004fin.2_Intron|SRPK3_uc004fim.2_Intron	NM_014370	NP_055185			serine arginine rich protein-specific kinase 3						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	153320929	153320929	+	Intron	DEL	T	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153320929delT	uc004fjv.2	-						MECP2_uc004fjw.2_Intron	NM_004992	NP_004983			methyl CpG binding protein 2 isoform 1						negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	heterochromatin|nucleus	double-stranded methylated DNA binding|protein domain specific binding|protein N-terminus binding|transcription corepressor activity				0	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	153368251	153368252	+	IGR	DEL	AA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153368251_153368252delAA								MECP2 (5063 upstream) : OPN1LW (41473 downstream)																																			---	---	---	---
BRCC3	79184	broad.mit.edu	37	X	154350402	154350405	+	3'UTR	DEL	AAAA	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154350402_154350405delAAAA	uc004fna.2	+	12					BRCC3_uc004fnb.2_3'UTR	NM_024332	NP_077308			BRCA1/BRCA2-containing complex, subunit 3						double-strand break repair|G2/M transition DNA damage checkpoint|histone H2A K63-linked deubiquitination|positive regulation of DNA repair|response to X-ray	BRCA1-A complex|BRISC complex|nuclear ubiquitin ligase complex	enzyme regulator activity|metal ion binding|metallopeptidase activity|polyubiquitin binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			lung(3)|ovary(1)|large_intestine(1)|breast(1)	6	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	9981809	9981809	+	IGR	DEL	C	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9981809delC								TTTY22 (330955 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	13262505	13262506	+	IGR	DEL	TG	-	-			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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	13472490	13472491	+	IGR	INS	-	G	G	rs113165162		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13472490_13472491insG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	59006978	59006978	+	IGR	DEL	A	-	-	rs140439618		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59006978delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	59024711	59024714	+	IGR	DEL	TAAT	-	-	rs140947617		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59024711_59024714delTAAT								None (None upstream) : None (None downstream)																																			---	---	---	---
MMEL1	79258	broad.mit.edu	37	1	2523073	2523073	+	Splice_Site	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2523073C>A	uc001ajy.2	-	23	2378	c.2164_splice	c.e23-1	p.V722_splice	MMEL1_uc009vlg.1_Splice_Site	NM_033467	NP_258428			membrane metallo-endopeptidase-like 1						proteolysis	extracellular region|integral to membrane|intracellular membrane-bounded organelle	metal ion binding|metalloendopeptidase activity				0	all_cancers(77;0.000233)|all_epithelial(69;8.55e-05)|all_lung(157;0.0228)|Lung NSC(156;0.0402)|Ovarian(185;0.0634)	all_epithelial(116;1.03e-20)|all_lung(118;5.15e-09)|Lung NSC(185;9.02e-07)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;8.52e-23)|GBM - Glioblastoma multiforme(42;1.49e-08)|Colorectal(212;4.79e-05)|COAD - Colon adenocarcinoma(227;0.000213)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00219)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.131)														---	---	---	---
C1orf174	339448	broad.mit.edu	37	1	3807490	3807490	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3807490T>C	uc001alf.2	-	3	368	c.261A>G	c.(259-261)ACA>ACG	p.T87T	C1orf174_uc009vls.2_RNA	NM_207356	NP_997239	Q8IYL3	CA174_HUMAN	hypothetical protein LOC339448	87											0	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_cancers(23;5.09e-25)|all_epithelial(116;9.35e-17)|all_lung(118;1.09e-06)|Lung NSC(185;0.000139)|all_neural(13;0.00287)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0219)|all_hematologic(16;0.027)|Colorectal(325;0.0276)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127)		Epithelial(90;1.55e-39)|OV - Ovarian serous cystadenocarcinoma(86;5.99e-23)|GBM - Glioblastoma multiforme(42;2.22e-17)|Colorectal(212;1.08e-05)|COAD - Colon adenocarcinoma(227;5.49e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.000365)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.19)														---	---	---	---
TNFRSF25	8718	broad.mit.edu	37	1	6522198	6522198	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6522198G>A	uc001ane.2	-	9	869	c.781C>T	c.(781-783)CTT>TTT	p.L261F	TNFRSF25_uc001ana.2_Missense_Mutation_p.L78F|TNFRSF25_uc001anb.2_RNA|TNFRSF25_uc001anc.2_RNA|TNFRSF25_uc001and.2_Missense_Mutation_p.L34F|TNFRSF25_uc009vlz.2_RNA|TNFRSF25_uc001anf.2_Missense_Mutation_p.L224F|TNFRSF25_uc001ang.2_Missense_Mutation_p.L216F|TNFRSF25_uc001anh.2_Missense_Mutation_p.L270F	NM_003790	NP_003781	Q93038	TNR25_HUMAN	tumor necrosis factor receptor superfamily,	261	Cytoplasmic (Potential).				apoptosis|induction of apoptosis by extracellular signals	cytosol|extracellular region|integral to plasma membrane	tumor necrosis factor receptor activity			central_nervous_system(2)|breast(1)	3	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Acute lymphoblastic leukemia(12;0.00157)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;4.58e-35)|GBM - Glioblastoma multiforme(13;3.06e-27)|Colorectal(212;6.01e-08)|COAD - Colon adenocarcinoma(227;1.3e-05)|Kidney(185;4.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000871)|BRCA - Breast invasive adenocarcinoma(365;0.00105)|STAD - Stomach adenocarcinoma(132;0.00158)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
PER3	8863	broad.mit.edu	37	1	7880708	7880708	+	Intron	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7880708A>G	uc001aoo.2	+						PER3_uc009vmg.1_Intron|PER3_uc009vmh.1_Intron|PER3_uc001aop.2_Intron|PER3_uc010nzw.1_Intron	NM_016831	NP_058515			period 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	signal transducer activity			ovary(1)|pancreas(1)|skin(1)	3	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
UBE4B	10277	broad.mit.edu	37	1	10186933	10186933	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10186933A>G	uc001aqs.3	+	11	2349	c.1636A>G	c.(1636-1638)ATG>GTG	p.M546V	UBE4B_uc001aqr.3_Missense_Mutation_p.M417V|UBE4B_uc010oai.1_RNA|UBE4B_uc010oaj.1_Missense_Mutation_p.M1V	NM_001105562	NP_001099032	O95155	UBE4B_HUMAN	ubiquitination factor E4B isoform 1	546					apoptosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to UV	cytoplasm|ubiquitin ligase complex	enzyme binding			ovary(2)|skin(2)	4		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)														---	---	---	---
MTOR	2475	broad.mit.edu	37	1	11303326	11303326	+	Silent	SNP	A	G	G	rs142286050		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11303326A>G	uc001asd.2	-	9	1378	c.1257T>C	c.(1255-1257)CAT>CAC	p.H419H		NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated	419					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																		---	---	---	---
FBXO6	26270	broad.mit.edu	37	1	11733844	11733844	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11733844G>T	uc001aso.2	+	6	984	c.818G>T	c.(817-819)GGG>GTG	p.G273V		NM_018438	NP_060908	Q9NRD1	FBX6_HUMAN	F-box only protein 6	273					DNA damage checkpoint|DNA repair|ER-associated protein catabolic process|response to unfolded protein|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cytoplasm|SCF ubiquitin ligase complex	glycoprotein binding			lung(1)	1	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.25e-06)|COAD - Colon adenocarcinoma(227;0.000251)|BRCA - Breast invasive adenocarcinoma(304;0.000297)|Kidney(185;0.000747)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
VPS13D	55187	broad.mit.edu	37	1	12336999	12336999	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12336999G>A	uc001atv.2	+	19	3495	c.3354G>A	c.(3352-3354)ACG>ACA	p.T1118T	VPS13D_uc001atw.2_Silent_p.T1118T|VPS13D_uc001atx.2_Silent_p.T306T	NM_015378	NP_056193	Q5THJ4	VP13D_HUMAN	vacuolar protein sorting 13D isoform 1	1118					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)														---	---	---	---
SPEN	23013	broad.mit.edu	37	1	16256462	16256462	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16256462C>T	uc001axk.1	+	11	3931	c.3727C>T	c.(3727-3729)CGG>TGG	p.R1243W	SPEN_uc010obp.1_Missense_Mutation_p.R1202W	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	1243					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)														---	---	---	---
SPEN	23013	broad.mit.edu	37	1	16257648	16257648	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16257648G>A	uc001axk.1	+	11	5117	c.4913G>A	c.(4912-4914)GGG>GAG	p.G1638E	SPEN_uc010obp.1_Missense_Mutation_p.G1597E	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	1638					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	16459688	16459688	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16459688G>A	uc001aya.1	-	11	2177	c.2040C>T	c.(2038-2040)GGC>GGT	p.G680G		NM_004431	NP_004422	P29317	EPHA2_HUMAN	ephrin receptor EphA2 precursor	680	Mediates interaction with ARHGEF16 and ELMO2.|Protein kinase.|Cytoplasmic (Potential).				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)													---	---	---	---
C1orf144	26099	broad.mit.edu	37	1	16721628	16721628	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16721628G>A	uc001aym.3	+	4	622	c.452G>A	c.(451-453)CGC>CAC	p.R151H	C1orf144_uc010ocb.1_Silent_p.A114A|C1orf144_uc001ayi.3_Missense_Mutation_p.R132H|C1orf144_uc001ayk.3_Missense_Mutation_p.R131H	NM_001114600	NP_001108072	Q7Z422	CA144_HUMAN	putative MAPK activating protein PM20,PM21	151											0		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(227;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;4.12e-05)|Kidney(64;0.00018)|KIRC - Kidney renal clear cell carcinoma(64;0.00267)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
KLHDC7A	127707	broad.mit.edu	37	1	18808314	18808314	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18808314G>A	uc001bax.2	+	1	891	c.839G>A	c.(838-840)GGG>GAG	p.G280E	KLHDC7A_uc009vpg.2_Missense_Mutation_p.G62E	NM_152375	NP_689588	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	280						integral to membrane				ovary(2)|upper_aerodigestive_tract(1)	3		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
UBR4	23352	broad.mit.edu	37	1	19421518	19421518	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19421518G>A	uc001bbi.2	-	94	13632	c.13628C>T	c.(13627-13629)GCC>GTC	p.A4543V	UBR4_uc010ocv.1_Intron|UBR4_uc009vph.2_Missense_Mutation_p.A177V|UBR4_uc010ocw.1_Missense_Mutation_p.A207V|UBR4_uc001bbg.2_Missense_Mutation_p.A254V|UBR4_uc001bbh.2_Missense_Mutation_p.A252V	NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600	4543					interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)|skin(2)	25		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)														---	---	---	---
UBXN10	127733	broad.mit.edu	37	1	20517188	20517188	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20517188G>A	uc001bdb.2	+	2	218	c.134G>A	c.(133-135)CGG>CAG	p.R45Q		NM_152376	NP_689589	Q96LJ8	UBX10_HUMAN	UBX domain protein 10	45										ovary(1)	1																		---	---	---	---
PINK1	65018	broad.mit.edu	37	1	20971064	20971064	+	Silent	SNP	G	A	A	rs148144773		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20971064G>A	uc001bdm.2	+	4	952	c.858G>A	c.(856-858)CCG>CCA	p.P286P		NM_032409	NP_115785	Q9BXM7	PINK1_HUMAN	PTEN induced putative kinase 1 precursor	286	Protein kinase.|Cytoplasmic (Potential).				cell death|intracellular protein kinase cascade|mitochondrion degradation|peptidyl-serine phosphorylation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of release of cytochrome c from mitochondria|regulation of protein complex assembly|regulation of protein ubiquitination|response to stress	cytosol|integral to membrane|mitochondrial outer membrane	ATP binding|C3HC4-type RING finger domain binding|calcium-dependent protein kinase activity|magnesium ion binding|protein serine/threonine kinase activity|ubiquitin protein ligase binding			ovary(2)|central_nervous_system(1)	3		all_lung(284;2.72e-05)|Lung NSC(340;2.94e-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;0.0182)|COAD - Colon adenocarcinoma(152;1.21e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000146)|Kidney(64;0.000182)|GBM - Glioblastoma multiforme(114;0.000497)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)														---	---	---	---
NBPF3	84224	broad.mit.edu	37	1	21771655	21771655	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21771655G>A	uc001ber.2	+	2	426	c.76G>A	c.(76-78)GCA>ACA	p.A26T	NBPF3_uc001bes.2_5'UTR|NBPF3_uc009vqb.2_Missense_Mutation_p.A26T|NBPF3_uc010odm.1_Missense_Mutation_p.A26T	NM_032264	NP_115640	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3	26						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)														---	---	---	---
HSPG2	3339	broad.mit.edu	37	1	22160092	22160092	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22160092G>A	uc001bfj.2	-	79	10886	c.10846C>T	c.(10846-10848)CCA>TCA	p.P3616S	HSPG2_uc001bfi.2_5'Flank|HSPG2_uc009vqd.2_Missense_Mutation_p.P3617S	NM_005529	NP_005520	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2 precursor	3616	Ig-like C2-type 22.				angiogenesis|cell adhesion|lipid metabolic process|lipoprotein metabolic process	basement membrane|extracellular space|plasma membrane	protein C-terminus binding			ovary(5)|large_intestine(2)|central_nervous_system(1)|skin(1)	9		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Becaplermin(DB00102)|Palifermin(DB00039)													---	---	---	---
EPHB2	2048	broad.mit.edu	37	1	23191577	23191577	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23191577G>A	uc009vqj.1	+	5	1320	c.1175G>A	c.(1174-1176)CGC>CAC	p.R392H	EPHB2_uc001bge.2_Missense_Mutation_p.R392H|EPHB2_uc001bgf.2_Missense_Mutation_p.R392H|EPHB2_uc010odu.1_Missense_Mutation_p.R392H|hsa-mir-4253|MI0015860_5'Flank	NM_017449	NP_059145	P29323	EPHB2_HUMAN	ephrin receptor EphB2 isoform 1 precursor	392	Extracellular (Potential).|Fibronectin type-III 1.				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				---	---	---	---
HTR1D	3352	broad.mit.edu	37	1	23519991	23519991	+	Missense_Mutation	SNP	G	A	A	rs138622697	byFrequency	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23519991G>A	uc001bgn.2	-	1	1232	c.722C>T	c.(721-723)ACG>ATG	p.T241M		NM_000864	NP_000855	P28221	5HT1D_HUMAN	5-hydroxytryptamine (serotonin) receptor 1D	241	Cytoplasmic (By similarity).				G-protein signaling, coupled to cyclic nucleotide second messenger|intestine smooth muscle contraction|synaptic transmission	integral to plasma membrane	serotonin receptor activity				0		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000779)|all_lung(284;0.00135)|Breast(348;0.0385)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0561)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;4.69e-27)|Colorectal(126;4.86e-08)|COAD - Colon adenocarcinoma(152;2.86e-06)|GBM - Glioblastoma multiforme(114;0.00012)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(1967;0.00122)|STAD - Stomach adenocarcinoma(196;0.0123)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.083)|LUSC - Lung squamous cell carcinoma(448;0.185)	Almotriptan(DB00918)|Dihydroergotamine(DB00320)|Eletriptan(DB00216)|Ergotamine(DB00696)|Frovatriptan(DB00998)|Naratriptan(DB00952)|Rizatriptan(DB00953)|Sumatriptan(DB00669)|Tegaserod(DB01079)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)													---	---	---	---
SLC30A2	7780	broad.mit.edu	37	1	26369997	26369997	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26369997G>A	uc001blh.1	-	3	534	c.317C>T	c.(316-318)ACG>ATG	p.T106M	SLC30A2_uc001blg.1_Missense_Mutation_p.T155M	NM_032513	NP_115902	Q9BRI3	ZNT2_HUMAN	solute carrier family 30, member 2 isoform 2	106	Helical; (Potential).				positive regulation of sequestering of zinc ion|zinc ion transport	integral to membrane|late endosome|lysosomal membrane	cation transmembrane transporter activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;6.18e-05)|all_lung(284;9.43e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;7.09e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000728)|BRCA - Breast invasive adenocarcinoma(304;0.000969)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00614)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
CCDC21	64793	broad.mit.edu	37	1	26581810	26581810	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26581810T>C	uc001bls.1	+	4	488	c.357T>C	c.(355-357)CCT>CCC	p.P119P	CCDC21_uc001blr.2_Silent_p.P119P|CCDC21_uc010ofa.1_Silent_p.P68P	NM_022778	NP_073615	Q6P2H3	CEP85_HUMAN	coiled-coil domain containing 21	119						centrosome|nucleolus|spindle pole					0		all_cancers(24;7e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.6e-26)|Colorectal(126;1.65e-08)|COAD - Colon adenocarcinoma(152;9.48e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00155)|GBM - Glioblastoma multiforme(114;0.00917)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
CCDC21	64793	broad.mit.edu	37	1	26584680	26584680	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26584680G>A	uc001bls.1	+	6	1215	c.1084G>A	c.(1084-1086)GAA>AAA	p.E362K	CCDC21_uc001blr.2_Missense_Mutation_p.E362K|CCDC21_uc010ofa.1_Missense_Mutation_p.E311K	NM_022778	NP_073615	Q6P2H3	CEP85_HUMAN	coiled-coil domain containing 21	362	Potential.					centrosome|nucleolus|spindle pole					0		all_cancers(24;7e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.6e-26)|Colorectal(126;1.65e-08)|COAD - Colon adenocarcinoma(152;9.48e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00155)|GBM - Glioblastoma multiforme(114;0.00917)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
HDAC1	3065	broad.mit.edu	37	1	32796193	32796193	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32796193A>G	uc001bvb.1	+	8	807	c.744A>G	c.(742-744)GTA>GTG	p.V248V	HDAC1_uc010ohf.1_Silent_p.V219V|HDAC1_uc001bvc.1_Silent_p.V4V	NM_004964	NP_004955	Q13547	HDAC1_HUMAN	histone deacetylase 1	248	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)													---	---	---	---
TMEM54	113452	broad.mit.edu	37	1	33360993	33360993	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33360993C>T	uc001bwi.1	-	5	621	c.507G>A	c.(505-507)GCG>GCA	p.A169A	TMEM54_uc001bwj.1_Silent_p.A116A|TMEM54_uc001bwk.1_Silent_p.A149A	NM_033504	NP_277039	Q969K7	TMM54_HUMAN	transmembrane protein 54	169	Helical; (Potential).					integral to membrane					0		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)																---	---	---	---
DLGAP3	58512	broad.mit.edu	37	1	35351169	35351169	+	Silent	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35351169G>T	uc001byc.2	-	5	1824	c.1824C>A	c.(1822-1824)CCC>CCA	p.P608P		NM_001080418	NP_001073887	O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated	608					cell-cell signaling	cell junction|postsynaptic density|postsynaptic membrane				ovary(3)	3		Myeloproliferative disorder(586;0.0393)																---	---	---	---
ZMYM4	9202	broad.mit.edu	37	1	35824963	35824963	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35824963C>A	uc001byt.2	+	3	603	c.523C>A	c.(523-525)CTA>ATA	p.L175I	ZMYM4_uc009vuu.2_Missense_Mutation_p.L143I|ZMYM4_uc001byu.2_Intron|ZMYM4_uc009vuv.2_5'UTR	NM_005095	NP_005086	Q5VZL5	ZMYM4_HUMAN	zinc finger protein 262	175					multicellular organismal development		DNA binding|zinc ion binding			large_intestine(2)|ovary(1)|kidney(1)|skin(1)	5		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
ZC3H12A	80149	broad.mit.edu	37	1	37949111	37949111	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37949111C>T	uc001cbb.3	+	6	1849	c.1699C>T	c.(1699-1701)CAC>TAC	p.H567Y	ZC3H12A_uc001cbc.1_Missense_Mutation_p.H362Y	NM_025079	NP_079355	Q5D1E8	ZC12A_HUMAN	zinc finger CCCH-type containing 12A	567					angiogenesis|apoptosis|cell differentiation	cytoplasm|nucleus|plasma membrane	endonuclease activity|metal ion binding			ovary(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)																---	---	---	---
PABPC4	8761	broad.mit.edu	37	1	40029411	40029411	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40029411C>T	uc010oiv.1	-	12	2393	c.1495G>A	c.(1495-1497)GTT>ATT	p.V499I	PABPC4_uc001cdl.2_Missense_Mutation_p.V515I|PABPC4_uc001cdm.2_Missense_Mutation_p.V486I	NM_003819	NP_003810	Q13310	PABP4_HUMAN	poly A binding protein, cytoplasmic 4 isoform 2	499					blood coagulation|RNA catabolic process|RNA processing|translation	cytoplasm|ribonucleoprotein complex	nucleotide binding|poly(A) RNA binding|poly(U) RNA binding|protein binding				0	Lung NSC(20;1.55e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.89e-18)|Epithelial(16;6.17e-17)|all cancers(16;1.18e-15)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)															---	---	---	---
RLF	6018	broad.mit.edu	37	1	40702226	40702226	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40702226A>G	uc001cfc.3	+	8	1883	c.1852A>G	c.(1852-1854)AAA>GAA	p.K618E	RLF_uc001cfd.3_Missense_Mutation_p.K309E	NM_012421	NP_036553	Q13129	RLF_HUMAN	rearranged L-myc fusion	618					chromosome organization|DNA integration|DNA mediated transformation|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			ovary(2)|pancreas(1)	3	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)															---	---	---	---
PTPRF	5792	broad.mit.edu	37	1	44079382	44079382	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44079382A>G	uc001cjr.2	+	23	4407	c.4067A>G	c.(4066-4068)TAT>TGT	p.Y1356C	PTPRF_uc001cjs.2_Missense_Mutation_p.Y1347C|PTPRF_uc001cju.2_Missense_Mutation_p.Y745C|PTPRF_uc009vwt.2_Missense_Mutation_p.Y916C|PTPRF_uc001cjv.2_Missense_Mutation_p.Y827C|PTPRF_uc001cjw.2_Missense_Mutation_p.Y582C	NM_002840	NP_002831	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1356	Tyrosine-protein phosphatase 1.|Cytoplasmic (Potential).				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|skin(3)|lung(1)|kidney(1)|central_nervous_system(1)	10	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)																---	---	---	---
ST3GAL3	6487	broad.mit.edu	37	1	44365253	44365253	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44365253G>T	uc001ckc.2	+	9	775	c.598G>T	c.(598-600)GGC>TGC	p.G200C	ST3GAL3_uc010okj.1_RNA|ST3GAL3_uc001cjz.2_Missense_Mutation_p.G215C|ST3GAL3_uc001cka.2_Intron|ST3GAL3_uc001ckb.2_Missense_Mutation_p.G269C|ST3GAL3_uc001ckd.2_Missense_Mutation_p.G254C|ST3GAL3_uc001cke.2_Missense_Mutation_p.G184C|ST3GAL3_uc001ckf.2_Missense_Mutation_p.G238C|ST3GAL3_uc001ckg.2_Missense_Mutation_p.G200C|ST3GAL3_uc001ckh.2_Intron|ST3GAL3_uc001cki.2_Intron|ST3GAL3_uc009vwv.2_Missense_Mutation_p.G200C|ST3GAL3_uc001ckj.2_RNA|ST3GAL3_uc009vww.2_Intron|ST3GAL3_uc001ckk.2_Missense_Mutation_p.G169C|ST3GAL3_uc009vwy.2_Missense_Mutation_p.G106C|ST3GAL3_uc009vwx.2_RNA|ST3GAL3_uc001ckm.2_Intron|ST3GAL3_uc001ckl.2_Intron|ST3GAL3_uc009vwz.2_Intron|ST3GAL3_uc001ckn.2_Intron|ST3GAL3_uc001ckp.2_Intron|ST3GAL3_uc001cko.2_Missense_Mutation_p.G184C|ST3GAL3_uc009vxa.2_5'UTR|ST3GAL3_uc001ckq.2_Intron|ST3GAL3_uc001ckr.2_Missense_Mutation_p.G153C|ST3GAL3_uc009vxb.2_Intron	NM_006279	NP_006270	Q11203	SIAT6_HUMAN	sialyltransferase 6 isoform j	200	Lumenal (Potential).				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)																---	---	---	---
KIF2C	11004	broad.mit.edu	37	1	45213333	45213333	+	Missense_Mutation	SNP	C	T	T	rs145490610		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45213333C>T	uc001cmg.3	+	4	392	c.277C>T	c.(277-279)CGG>TGG	p.R93W	KIF2C_uc010olb.1_Missense_Mutation_p.R93W|KIF2C_uc010olc.1_Translation_Start_Site|KIF2C_uc001cmh.3_Missense_Mutation_p.R39W	NM_006845	NP_006836	Q99661	KIF2C_HUMAN	kinesin family member 2C	93	Globular (Potential).				blood coagulation|cell division|cell proliferation|chromosome segregation|establishment or maintenance of microtubule cytoskeleton polarity|microtubule depolymerization|microtubule-based movement|mitotic prometaphase|regulation of chromosome segregation	condensed chromosome kinetochore|cytosol|kinesin complex|microtubule|nucleus	ATP binding|centromeric DNA binding|microtubule motor activity|microtubule plus-end binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
GPBP1L1	60313	broad.mit.edu	37	1	46095334	46095334	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46095334C>A	uc001coq.2	-	12	2547	c.1186G>T	c.(1186-1188)GGT>TGT	p.G396C	GPBP1L1_uc001coo.2_Missense_Mutation_p.G140C	NM_021639	NP_067652	Q9HC44	GPBL1_HUMAN	GC-rich promoter binding protein 1-like 1	396					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
RAD54L	8438	broad.mit.edu	37	1	46715676	46715676	+	Missense_Mutation	SNP	C	A	A	rs112896925	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46715676C>A	uc009vye.2	+	4	209	c.95C>A	c.(94-96)CCT>CAT	p.P32H	RAD54L_uc001cpl.2_Missense_Mutation_p.P32H	NM_001142548	NP_001136020	Q92698	RAD54_HUMAN	RAD54-like protein	32					meiosis	nucleus	ATP binding|DNA binding|helicase activity			ovary(2)|skin(1)	3	Acute lymphoblastic leukemia(166;0.155)	Breast(1374;0.0634)		KIRC - Kidney renal clear cell carcinoma(1967;0.000896)									Direct_reversal_of_damage|Homologous_recombination					---	---	---	---
LRRC41	10489	broad.mit.edu	37	1	46751116	46751116	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46751116T>C	uc001cpn.2	-	4	1457	c.1413A>G	c.(1411-1413)CCA>CCG	p.P471P	LRRC41_uc010omb.1_Silent_p.P471P|LRRC41_uc001cpo.1_Silent_p.P471P	NM_006369	NP_006360	Q15345	LRC41_HUMAN	MUF1 protein	471										ovary(2)|breast(1)|pancreas(1)	4	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
SPATA6	54558	broad.mit.edu	37	1	48825450	48825450	+	Intron	SNP	A	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48825450A>T	uc001crr.1	-						SPATA6_uc001crs.1_Intron|SPATA6_uc010omv.1_Intron	NM_019073	NP_061946			spermatogenesis associated 6 precursor						cell differentiation|multicellular organismal development|spermatogenesis	extracellular region				ovary(1)	1																		---	---	---	---
NRD1	4898	broad.mit.edu	37	1	52306066	52306066	+	Missense_Mutation	SNP	T	A	A	rs72496486		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52306066T>A	uc001ctc.3	-	2	784	c.462A>T	c.(460-462)GAA>GAT	p.E154D	NRD1_uc009vzb.2_Translation_Start_Site|NRD1_uc001ctd.3_Missense_Mutation_p.E154D|NRD1_uc001cte.2_Missense_Mutation_p.E22D|NRD1_uc001ctf.2_Missense_Mutation_p.E154D|NRD1_uc010ong.1_RNA|NRD1_uc009vzc.1_Missense_Mutation_p.E22D|NRD1_uc001ctg.1_5'Flank	NM_002525	NP_002516	O43847	NRDC_HUMAN	nardilysin isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					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																		---	---	---	---
ZFYVE9	9372	broad.mit.edu	37	1	52759349	52759349	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52759349C>T	uc001cto.2	+	11	3422	c.3250C>T	c.(3250-3252)CTT>TTT	p.L1084F	ZFYVE9_uc001ctp.2_Missense_Mutation_p.L1025F	NM_004799	NP_004790	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9 isoform 3	1084					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																		---	---	---	---
GPX7	2882	broad.mit.edu	37	1	53072458	53072458	+	Missense_Mutation	SNP	G	A	A	rs140772221		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53072458G>A	uc001cue.2	+	2	280	c.241G>A	c.(241-243)GTG>ATG	p.V81M		NM_015696	NP_056511	Q96SL4	GPX7_HUMAN	glutathione peroxidase 7 precursor	81					response to oxidative stress	extracellular region	glutathione peroxidase activity				0					Glutathione(DB00143)													---	---	---	---
CDCP2	200008	broad.mit.edu	37	1	54610186	54610186	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54610186G>A	uc001cwv.1	-	2	1228	c.380C>T	c.(379-381)TCG>TTG	p.S127L		NM_201546	NP_963840	Q5VXM1	CDCP2_HUMAN	CUB domain containing protein 2 precursor	127	CUB 1.					extracellular region				ovary(1)	1																		---	---	---	---
PARS2	25973	broad.mit.edu	37	1	55223931	55223931	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55223931T>G	uc001cxy.2	-	2	987	c.904A>C	c.(904-906)ACC>CCC	p.T302P		NM_152268	NP_689481	Q7L3T8	SYPM_HUMAN	prolyl-tRNA synthetase (mitochondrial)(putative)	302					prolyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|proline-tRNA ligase activity			ovary(2)	2					L-Proline(DB00172)													---	---	---	---
DAB1	1600	broad.mit.edu	37	1	58522087	58522087	+	Intron	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58522087G>T	uc001cys.1	-						DAB1_uc001cyt.1_Intron	NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
DOCK7	85440	broad.mit.edu	37	1	62958419	62958419	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62958419C>A	uc001daq.2	-	41	5324	c.5290G>T	c.(5290-5292)GGA>TGA	p.G1764*	DOCK7_uc001dan.2_Nonsense_Mutation_p.G1625*|DOCK7_uc001dao.2_Nonsense_Mutation_p.G1625*|DOCK7_uc001dap.2_Nonsense_Mutation_p.G1742*|DOCK7_uc001dam.2_Nonsense_Mutation_p.G944*|DOCK7_uc010oov.1_Nonsense_Mutation_p.G503*	NM_033407	NP_212132	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	1773	DHR-2.				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																		---	---	---	---
IL23R	149233	broad.mit.edu	37	1	67666515	67666515	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67666515T>C	uc001ddo.2	+	5	672	c.587T>C	c.(586-588)GTC>GCC	p.V196A	IL23R_uc009waz.2_5'UTR|IL23R_uc001ddp.2_RNA|IL23R_uc010opi.1_RNA|IL23R_uc010opj.1_Intron|IL23R_uc010opk.1_Missense_Mutation_p.V153A|IL23R_uc010opl.1_Intron|IL23R_uc010opm.1_RNA|IL23R_uc001ddq.2_Intron|IL23R_uc010opn.1_Missense_Mutation_p.V41A|IL23R_uc001ddr.2_RNA|IL23R_uc010opo.1_Missense_Mutation_p.V55A|IL23R_uc010opp.1_Intron|IL23R_uc010opq.1_Missense_Mutation_p.V55A|IL23R_uc010opr.1_RNA|IL23R_uc010ops.1_5'UTR|IL23R_uc010opt.1_5'UTR|IL23R_uc010opu.1_5'UTR|IL23R_uc010opv.1_Missense_Mutation_p.V55A|IL23R_uc010opw.1_Intron|IL23R_uc010opx.1_Intron|IL23R_uc010opy.1_5'UTR|IL23R_uc010opz.1_Intron|IL23R_uc010oqa.1_5'UTR|IL23R_uc010oqb.1_Missense_Mutation_p.V55A|IL23R_uc010oqc.1_Intron|IL23R_uc010oqd.1_Intron|IL23R_uc010oqe.1_5'UTR|IL23R_uc010oqf.1_5'UTR|IL23R_uc010oqg.1_5'UTR|IL23R_uc010oqh.1_Intron	NM_144701	NP_653302	Q5VWK5	IL23R_HUMAN	interleukin 23 receptor precursor	196	Extracellular (Potential).|Fibronectin type-III 1.				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																		---	---	---	---
LRRIQ3	127255	broad.mit.edu	37	1	74492654	74492654	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74492654C>T	uc001dfy.3	-						LRRIQ3_uc001dfz.3_Intron	NM_001105659	NP_001099129			leucine-rich repeats and IQ motif containing 3											ovary(2)	2																		---	---	---	---
TTLL7	79739	broad.mit.edu	37	1	84383293	84383293	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84383293T>C	uc001djc.2	-	14	1977	c.1581A>G	c.(1579-1581)GGA>GGG	p.G527G	TTLL7_uc001djb.2_RNA|TTLL7_uc001djd.2_RNA|TTLL7_uc001dje.2_RNA|TTLL7_uc001djf.2_RNA|TTLL7_uc001djg.2_RNA	NM_024686	NP_078962	Q6ZT98	TTLL7_HUMAN	tubulin tyrosine ligase-like family, member 7	527					cell differentiation|nervous system development|protein modification process	cilium|dendrite|microtubule basal body|perikaryon	tubulin-tyrosine ligase activity			ovary(1)	1				all cancers(265;0.0126)|Epithelial(280;0.0372)|OV - Ovarian serous cystadenocarcinoma(397;0.16)														---	---	---	---
CLCA2	9635	broad.mit.edu	37	1	86890045	86890045	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86890045G>T	uc001dlr.3	+	1	277	c.115G>T	c.(115-117)GGG>TGG	p.G39W		NM_006536	NP_006527	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2 precursor	39	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)														---	---	---	---
GBP7	388646	broad.mit.edu	37	1	89613377	89613377	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89613377A>G	uc001dna.2	-	8	1377	c.1238T>C	c.(1237-1239)CTT>CCT	p.L413P	GBP2_uc001dmy.1_RNA	NM_207398	NP_997281	Q8N8V2	GBP7_HUMAN	guanylate binding protein 4-like	413						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)														---	---	---	---
GBP6	163351	broad.mit.edu	37	1	89834253	89834253	+	Missense_Mutation	SNP	G	A	A	rs139938902	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89834253G>A	uc001dnf.2	+	2	417	c.143G>A	c.(142-144)CGT>CAT	p.R48H	GBP6_uc010ost.1_Intron	NM_198460	NP_940862	Q6ZN66	GBP6_HUMAN	guanylate binding protein family, member 6	48	GTP (By similarity).						GTP binding|GTPase activity			ovary(2)	2		Lung NSC(277;0.0908)		all cancers(265;0.0108)|Epithelial(280;0.0398)														---	---	---	---
BRDT	676	broad.mit.edu	37	1	92445187	92445187	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92445187G>A	uc001dok.3	+	8	1509	c.1160G>A	c.(1159-1161)TGT>TAT	p.C387Y	BRDT_uc001dol.3_Missense_Mutation_p.C387Y|BRDT_uc010osz.1_Missense_Mutation_p.C391Y|BRDT_uc009wdf.2_Missense_Mutation_p.C314Y|BRDT_uc010ota.1_Missense_Mutation_p.C341Y|BRDT_uc010otb.1_Missense_Mutation_p.C341Y|BRDT_uc001dom.3_Missense_Mutation_p.C387Y	NM_207189	NP_997072	Q58F21	BRDT_HUMAN	testis-specific bromodomain protein	387					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein serine/threonine kinase activity|transcription coactivator activity			stomach(2)|ovary(1)|lung(1)	4		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)														---	---	---	---
PRPF38B	55119	broad.mit.edu	37	1	109238744	109238744	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109238744G>A	uc001dvv.3	+	3	707	c.425G>A	c.(424-426)CGA>CAA	p.R142Q	PRPF38B_uc001dvw.3_Missense_Mutation_p.R31Q|PRPF38B_uc010ouz.1_5'UTR	NM_018061	NP_060531	Q5VTL8	PR38B_HUMAN	PRP38 pre-mRNA processing factor 38 (yeast)	142					mRNA processing|RNA splicing	spliceosomal complex					0		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0149)|Lung(183;0.0888)|COAD - Colon adenocarcinoma(174;0.113)|Epithelial(280;0.161)														---	---	---	---
GPSM2	29899	broad.mit.edu	37	1	109466694	109466694	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109466694G>A	uc010ovc.1	+	14	2169	c.1673G>A	c.(1672-1674)CGT>CAT	p.R558H	AKNAD1_uc010ovb.1_Intron|GPSM2_uc010ovd.1_Missense_Mutation_p.R558H|GPSM2_uc010ove.1_Missense_Mutation_p.R558H	NM_013296	NP_037428	P81274	GPSM2_HUMAN	LGN protein	558	GoLoco 2.				G-protein coupled receptor protein signaling pathway	cell cortex|nucleus	GTPase activator activity|identical protein binding			central_nervous_system(1)	1		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0353)|Lung(183;0.0984)|COAD - Colon adenocarcinoma(174;0.129)|Epithelial(280;0.175)|all cancers(265;0.209)														---	---	---	---
WDR47	22911	broad.mit.edu	37	1	109514188	109514188	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109514188A>G	uc001dwj.2	-	15	3000	c.2624T>C	c.(2623-2625)CTC>CCC	p.L875P	WDR47_uc001dwl.2_Missense_Mutation_p.L883P|WDR47_uc001dwi.2_Missense_Mutation_p.L876P|WDR47_uc010ovf.1_Missense_Mutation_p.L800P	NM_001142551	NP_001136023	O94967	WDR47_HUMAN	WD repeat domain 47 isoform 3	875	WD 6.									ovary(1)	1		all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822)		Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244)														---	---	---	---
AMIGO1	57463	broad.mit.edu	37	1	110050068	110050068	+	Silent	SNP	C	T	T	rs142627495		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110050068C>T	uc001dxx.3	-	2	1849	c.1467G>A	c.(1465-1467)ACG>ACA	p.T489T		NM_020703	NP_065754	Q86WK6	AMGO1_HUMAN	AMIGO protein precursor	489	Cytoplasmic (Potential).				axonal fasciculation|heterophilic cell-cell adhesion|homophilic cell adhesion|myelination|positive regulation of axonogenesis	axon|integral to membrane				ovary(1)|breast(1)	2		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Colorectal(144;0.0129)|Lung(183;0.0182)|Epithelial(280;0.046)|all cancers(265;0.0492)|READ - Rectum adenocarcinoma(129;0.0689)|LUSC - Lung squamous cell carcinoma(189;0.227)														---	---	---	---
AMPD2	271	broad.mit.edu	37	1	110170532	110170532	+	Intron	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110170532C>A	uc009wfh.1	+						AMPD2_uc009wfg.1_Intron|AMPD2_uc001dyb.1_Intron|AMPD2_uc001dyc.1_Intron|AMPD2_uc010ovr.1_Intron|AMPD2_uc010ovs.1_Intron|AMPD2_uc001dyd.1_Intron|AMPD2_uc001dye.1_5'Flank	NM_004037	NP_004028			adenosine monophosphate deaminase 2 (isoform L)						purine base metabolic process|purine ribonucleoside monophosphate biosynthetic process|purine-containing compound salvage	cytosol	AMP deaminase activity|metal ion binding			ovary(2)|breast(1)	3		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Lung(183;0.0425)|all cancers(265;0.0884)|Colorectal(144;0.109)|Epithelial(280;0.111)|LUSC - Lung squamous cell carcinoma(189;0.228)														---	---	---	---
OVGP1	5016	broad.mit.edu	37	1	111968072	111968072	+	Intron	SNP	A	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111968072A>T	uc001eba.2	-						OVGP1_uc001eaz.2_Missense_Mutation_p.S46T|OVGP1_uc010owb.1_Intron|OVGP1_uc010owc.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)														---	---	---	---
ST7L	54879	broad.mit.edu	37	1	113068681	113068681	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113068681T>C	uc001ecd.2	-	15	1987	c.1682A>G	c.(1681-1683)AAT>AGT	p.N561S	ST7L_uc009wgh.2_RNA|ST7L_uc001ecc.2_Missense_Mutation_p.N378S|ST7L_uc010owg.1_Missense_Mutation_p.N496S|ST7L_uc010owh.1_Missense_Mutation_p.N355S|ST7L_uc001ece.2_Missense_Mutation_p.N530S|ST7L_uc001ecf.2_Missense_Mutation_p.N544S|ST7L_uc001ecg.2_RNA	NM_017744	NP_060214	Q8TDW4	ST7L_HUMAN	suppression of tumorigenicity 7-like isoform 1	561					negative regulation of cell growth	integral to membrane	binding				0	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
ST7L	54879	broad.mit.edu	37	1	113084607	113084607	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113084607T>G	uc001ecd.2	-	14	1900	c.1595A>C	c.(1594-1596)CAG>CCG	p.Q532P	ST7L_uc009wgh.2_RNA|ST7L_uc001ecc.2_Missense_Mutation_p.Q349P|ST7L_uc010owg.1_Missense_Mutation_p.Q467P|ST7L_uc010owh.1_Missense_Mutation_p.Q326P|ST7L_uc001ece.2_Missense_Mutation_p.Q501P|ST7L_uc001ecf.2_Missense_Mutation_p.Q515P|ST7L_uc001ecg.2_RNA|ST7L_uc010owi.1_Missense_Mutation_p.Q467P|ST7L_uc001ech.2_Missense_Mutation_p.Q515P|ST7L_uc001eci.2_Missense_Mutation_p.Q532P|ST7L_uc009wgi.1_RNA	NM_017744	NP_060214	Q8TDW4	ST7L_HUMAN	suppression of tumorigenicity 7-like isoform 1	532					negative regulation of cell growth	integral to membrane	binding				0	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
MAGI3	260425	broad.mit.edu	37	1	114226088	114226088	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114226088G>T	uc001edk.2	+	21	4079	c.3898G>T	c.(3898-3900)GCT>TCT	p.A1300S	MAGI3_uc001edi.3_3'UTR|MAGI3_uc010owm.1_3'UTR|MAGI3_uc001edj.2_3'UTR|MAGI3_uc009wgo.2_RNA	NM_001142782	NP_001136254	Q5TCQ9	MAGI3_HUMAN	membrane-associated guanylate kinase-related  3	1325					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)														---	---	---	---
IGSF3	3321	broad.mit.edu	37	1	117122336	117122336	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117122336A>G	uc001egr.1	-	10	3717	c.3012T>C	c.(3010-3012)CCT>CCC	p.P1004P	IGSF3_uc001egq.1_Silent_p.P1024P	NM_001007237	NP_001007238	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3 isoform 2	1004	Ig-like C2-type 8.|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)														---	---	---	---
TTF2	8458	broad.mit.edu	37	1	117618032	117618032	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117618032C>A	uc001egy.2	+	5	846	c.826C>A	c.(826-828)CAG>AAG	p.Q276K	TTF2_uc001egx.1_Missense_Mutation_p.Q276K	NM_003594	NP_003585	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase	276					mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|termination of RNA polymerase II transcription	cytoplasm|spliceosomal complex|transcription elongation factor complex	ATP binding|ATP-dependent helicase activity|DNA binding|DNA-dependent ATPase activity|protein binding|zinc ion binding			ovary(1)	1	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)														---	---	---	---
TXNIP	10628	broad.mit.edu	37	1	145441002	145441002	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145441002C>T	uc001enn.3	+	7	1430	c.1089C>T	c.(1087-1089)ATC>ATT	p.I363I	NBPF10_uc001emp.3_Intron|TXNIP_uc001enm.1_Intron|TXNIP_uc010oys.1_Silent_p.I308I	NM_006472	NP_006463	Q9H3M7	TXNIP_HUMAN	thioredoxin interacting protein	363					cell cycle|keratinocyte differentiation|transcription, DNA-dependent		ubiquitin protein ligase binding			ovary(2)	2	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)																	---	---	---	---
ANKRD35	148741	broad.mit.edu	37	1	145561111	145561111	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145561111C>T	uc001eob.1	+	10	907	c.799C>T	c.(799-801)CCC>TCC	p.P267S	NBPF10_uc001emp.3_Intron|ANKRD35_uc010oyx.1_Missense_Mutation_p.P110S	NM_144698	NP_653299	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	267										ovary(4)|skin(1)	5	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)																	---	---	---	---
CHD1L	9557	broad.mit.edu	37	1	146757979	146757979	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146757979G>A	uc001epm.3	+	18	2086	c.2023G>A	c.(2023-2025)GCC>ACC	p.A675T	uc001epp.2_Intron|CHD1L_uc001epn.3_Missense_Mutation_p.A562T|CHD1L_uc010ozo.1_RNA|CHD1L_uc009wjg.2_RNA|CHD1L_uc009wjh.2_Missense_Mutation_p.A581T|CHD1L_uc010ozp.1_Missense_Mutation_p.A394T|CHD1L_uc001epo.3_Missense_Mutation_p.A471T|CHD1L_uc009wji.2_Missense_Mutation_p.A394T	NM_004284	NP_004275	Q86WJ1	CHD1L_HUMAN	chromodomain helicase DNA binding protein	675	Potential.				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)																	---	---	---	---
BCL9	607	broad.mit.edu	37	1	147090709	147090709	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147090709C>A	uc001epq.2	+	8	1488	c.748C>A	c.(748-750)CAG>AAG	p.Q250K	BCL9_uc010ozr.1_Missense_Mutation_p.Q176K	NM_004326	NP_004317	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	250	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								---	---	---	---
ADAMTSL4	54507	broad.mit.edu	37	1	150526522	150526522	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150526522G>A	uc001eux.2	+	6	1291	c.1055G>A	c.(1054-1056)TGG>TAG	p.W352*	ADAMTSL4_uc001euw.2_Nonsense_Mutation_p.W352*|ADAMTSL4_uc009wlw.2_Nonsense_Mutation_p.W352*|ADAMTSL4_uc010pcg.1_Nonsense_Mutation_p.W352*	NM_019032	NP_061905	Q6UY14	ATL4_HUMAN	thrombospondin repeat containing 1 isoform 1	352					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)															---	---	---	---
HRNR	388697	broad.mit.edu	37	1	152188379	152188379	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152188379C>A	uc001ezt.1	-	3	5802	c.5726G>T	c.(5725-5727)AGG>ATG	p.R1909M		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	1909	21.				keratinization		calcium ion binding|protein binding			skin(2)|ovary(1)	3	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)															---	---	---	---
HRNR	388697	broad.mit.edu	37	1	152192080	152192080	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152192080G>A	uc001ezt.1	-	3	2101	c.2025C>T	c.(2023-2025)TAC>TAT	p.Y675Y		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	675	6.				keratinization		calcium ion binding|protein binding			skin(2)|ovary(1)	3	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)															---	---	---	---
CRNN	49860	broad.mit.edu	37	1	152382288	152382288	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152382288G>A	uc001ezx.2	-	3	1344	c.1270C>T	c.(1270-1272)CGC>TGC	p.R424C		NM_016190	NP_057274	Q9UBG3	CRNN_HUMAN	cornulin	424					cell-cell adhesion|response to heat	cytoplasm|membrane	calcium ion binding			ovary(2)|skin(1)	3	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)															---	---	---	---
SPRR4	163778	broad.mit.edu	37	1	152944388	152944388	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152944388C>T	uc001fav.1	+	2	85	c.22C>T	c.(22-24)CGG>TGG	p.R8W		NM_173080	NP_775103	Q96PI1	SPRR4_HUMAN	small proline-rich protein 4	8	Gln-rich.				keratinization|peptide cross-linking	cell cortex					0	Lung NSC(65;1.46e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
INTS3	65123	broad.mit.edu	37	1	153735778	153735778	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153735778C>A	uc009wom.2	+	17	1927	c.1706C>A	c.(1705-1707)CCT>CAT	p.P569H	INTS3_uc001fct.2_Missense_Mutation_p.P569H|INTS3_uc001fcu.2_Missense_Mutation_p.P261H|INTS3_uc001fcv.2_Missense_Mutation_p.P363H|INTS3_uc010peb.1_Missense_Mutation_p.P363H|INTS3_uc001fcw.2_Missense_Mutation_p.P82H|INTS3_uc010pec.1_Missense_Mutation_p.P82H	NM_023015	NP_075391	Q68E01	INT3_HUMAN	integrator complex subunit 3	570					DNA repair|G2/M transition checkpoint|response to ionizing radiation|snRNA processing	integrator complex|SOSS complex	protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)															---	---	---	---
NUP210L	91181	broad.mit.edu	37	1	153974465	153974465	+	Intron	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153974465G>A	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)															---	---	---	---
UBAP2L	9898	broad.mit.edu	37	1	154226460	154226460	+	Silent	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154226460C>A	uc001fep.3	+	15	1916	c.1749C>A	c.(1747-1749)TCC>TCA	p.S583S	UBAP2L_uc009wot.2_Silent_p.S583S|UBAP2L_uc010pek.1_Silent_p.S575S|UBAP2L_uc010pel.1_Silent_p.S593S|UBAP2L_uc010pen.1_Silent_p.S497S|UBAP2L_uc001feq.2_5'Flank	NM_014847	NP_055662	Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like isoform a	583					binding of sperm to zona pellucida		protein binding			ovary(1)|central_nervous_system(1)	2	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)															---	---	---	---
ADAR	103	broad.mit.edu	37	1	154570423	154570423	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154570423T>C	uc001ffh.2	-	4	2015	c.1815A>G	c.(1813-1815)TCA>TCG	p.S605S	ADAR_uc001ffj.2_Silent_p.S605S|ADAR_uc001ffi.2_Silent_p.S605S|ADAR_uc001ffk.2_Silent_p.S310S	NM_001111	NP_001102	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific isoform a	605					adenosine to inosine editing|gene silencing by RNA|mRNA modification|mRNA processing|type I interferon-mediated signaling pathway	cytoplasm|nucleolus|nucleoplasm	DNA binding|double-stranded RNA adenosine deaminase activity|metal ion binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)														---	---	---	---
EFNA1	1942	broad.mit.edu	37	1	155106006	155106006	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155106006G>A	uc001fhh.2	+	3	521	c.416G>A	c.(415-417)CGC>CAC	p.R139H	RAG1AP1_uc010pey.1_5'Flank|EFNA1_uc001fhi.2_Intron|EFNA1_uc009wpd.1_RNA|RAG1AP1_uc001fhj.3_5'Flank|RAG1AP1_uc001fhk.3_5'Flank|RAG1AP1_uc001fhl.3_5'Flank	NM_004428	NP_004419	P20827	EFNA1_HUMAN	ephrin A1 isoform a precursor	139					angiogenesis|aortic valve morphogenesis|cell migration|cell-cell signaling|endocardial cushion to mesenchymal transition involved in heart valve formation|ephrin receptor signaling pathway|mitral valve morphogenesis|negative regulation of epithelial to mesenchymal transition|negative regulation of transcription from RNA polymerase II promoter|positive regulation of peptidyl-tyrosine phosphorylation|regulation of cell adhesion mediated by integrin|substrate adhesion-dependent cell spreading	extracellular region|integral to plasma membrane	ephrin receptor binding				0	all_epithelial(22;4.71e-30)|all_lung(78;3.15e-27)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;2.28e-10)|all cancers(21;6.16e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000395)|LUSC - Lung squamous cell carcinoma(543;0.193)															---	---	---	---
FCRL4	83417	broad.mit.edu	37	1	157551335	157551335	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157551335C>T	uc001fqw.2	-	7	1371	c.1235G>A	c.(1234-1236)CGT>CAT	p.R412H	FCRL4_uc010phy.1_RNA	NM_031282	NP_112572	Q96PJ5	FCRL4_HUMAN	Fc receptor-like 4 precursor	412	Cytoplasmic (Potential).					integral to membrane|plasma membrane	receptor activity			ovary(2)|kidney(1)|skin(1)	4	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.245)																---	---	---	---
CD1D	912	broad.mit.edu	37	1	158152779	158152779	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158152779G>A	uc001frr.2	+	5	1218	c.719G>A	c.(718-720)CGG>CAG	p.R240Q	CD1D_uc009wss.2_Intron	NM_001766	NP_001757	P15813	CD1D_HUMAN	CD1D antigen precursor	240	Ig-like.|Extracellular (Potential).				antigen processing and presentation, endogenous lipid antigen via MHC class Ib|detection of bacterium|innate immune response|interspecies interaction between organisms|positive regulation of innate immune response|T cell selection	endosome membrane|integral to plasma membrane|lysosomal membrane	beta-2-microglobulin binding|exogenous lipid antigen binding|histone binding			ovary(1)	1	all_hematologic(112;0.0378)																	---	---	---	---
OR10T2	128360	broad.mit.edu	37	1	158368812	158368812	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158368812A>C	uc010pih.1	-	1	445	c.445T>G	c.(445-447)TCA>GCA	p.S149A		NM_001004475	NP_001004475	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T,	149	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)	3	all_hematologic(112;0.0378)																	---	---	---	---
OR10R2	343406	broad.mit.edu	37	1	158449917	158449917	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158449917G>A	uc010pik.1	+	1	250	c.250G>A	c.(250-252)GGC>AGC	p.G84S	uc001fso.1_RNA	NM_001004472	NP_001004472	Q8NGX6	O10R2_HUMAN	olfactory receptor, family 10, subfamily R,	84	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(2)|skin(1)	3	all_hematologic(112;0.0378)																	---	---	---	---
FCER1A	2205	broad.mit.edu	37	1	159275942	159275942	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159275942G>A	uc001ftq.2	+	5	595	c.496G>A	c.(496-498)GCC>ACC	p.A166T		NM_002001	NP_001992	P12319	FCERA_HUMAN	Fc fragment of IgE, high affinity I, receptor	166	Ig-like 2.|Extracellular (Potential).					integral to plasma membrane				lung(2)|skin(2)|prostate(1)	5	all_hematologic(112;0.0429)				Benzylpenicilloyl Polylysine(DB00895)|Omalizumab(DB00043)													---	---	---	---
OR10J3	441911	broad.mit.edu	37	1	159284367	159284367	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159284367A>G	uc010piu.1	-	1	83	c.83T>C	c.(82-84)TTC>TCC	p.F28S		NM_001004467	NP_001004467	Q5JRS4	O10J3_HUMAN	olfactory receptor, family 10, subfamily J,	28	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	all_hematologic(112;0.0429)																	---	---	---	---
DCAF8	50717	broad.mit.edu	37	1	160187373	160187373	+	3'UTR	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160187373T>C	uc001fvo.2	-	14					DCAF8_uc001fvn.2_3'UTR|DCAF8_uc009wth.2_3'UTR|DCAF8_uc010pjb.1_3'UTR|DCAF8_uc010pjc.1_3'UTR	NM_015726	NP_056541			DDB1 and CUL4 associated factor 8							CUL4 RING ubiquitin ligase complex	protein binding			skin(2)	2																		---	---	---	---
CD84	8832	broad.mit.edu	37	1	160535290	160535290	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160535290C>T	uc001fwh.3	-	2	316	c.292G>A	c.(292-294)GAT>AAT	p.D98N	CD84_uc001fwf.3_Missense_Mutation_p.D98N|CD84_uc001fwg.3_Missense_Mutation_p.D98N|CD84_uc009wtn.2_Missense_Mutation_p.D98N|CD84_uc001fwi.3_Intron|CD84_uc001fwj.2_Missense_Mutation_p.D98N|CD84_uc001fwk.2_Missense_Mutation_p.D98N	NM_003874	NP_003865	Q9UIB8	SLAF5_HUMAN	CD84 molecule	98	Extracellular (Potential).				blood coagulation|defense response|homophilic cell adhesion|leukocyte migration	integral to plasma membrane	receptor activity			ovary(2)|central_nervous_system(1)|skin(1)	4	all_cancers(52;3.62e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)															---	---	---	---
LY9	4063	broad.mit.edu	37	1	160771647	160771647	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160771647C>T	uc001fwu.2	+						LY9_uc001fwt.2_Silent_p.S174S|LY9_uc010pjs.1_Intron|LY9_uc001fwv.2_Intron|LY9_uc001fww.2_Intron|LY9_uc001fwx.2_Intron|LY9_uc001fwy.1_Intron	NM_002348	NP_002339			lymphocyte antigen 9 isoform a						cell adhesion|immunoglobulin mediated immune response	integral to membrane				ovary(1)	1	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)															---	---	---	---
F5	2153	broad.mit.edu	37	1	169483668	169483668	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169483668T>C	uc001ggg.1	-	25	6703	c.6558A>G	c.(6556-6558)GGA>GGG	p.G2186G		NM_000130	NP_000121	P12259	FA5_HUMAN	coagulation factor V precursor	2186	F5/8 type C 2.				cell adhesion|platelet activation|platelet degranulation	plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	all_hematologic(923;0.208)				Drotrecogin alfa(DB00055)													---	---	---	---
SCYL3	57147	broad.mit.edu	37	1	169823591	169823591	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169823591T>C	uc001ggs.2	-	13	2187	c.1989A>G	c.(1987-1989)GTA>GTG	p.V663V	SCYL3_uc010plw.1_Silent_p.V255V|SCYL3_uc001ggt.2_Silent_p.V609V|SCYL3_uc001ggu.2_RNA	NM_181093	NP_851607	Q8IZE3	PACE1_HUMAN	SCY1-like 3 isoform 2	663	Interaction with EZR.				cell migration	Golgi apparatus|lamellipodium	ATP binding|protein binding|protein kinase activity			ovary(1)|skin(1)	2	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)																	---	---	---	---
GORAB	92344	broad.mit.edu	37	1	170508371	170508371	+	Missense_Mutation	SNP	C	T	T	rs141615202		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170508371C>T	uc001gha.2	+	2	184	c.157C>T	c.(157-159)CGT>TGT	p.R53C	GORAB_uc009wvw.2_Silent_p.D115D|GORAB_uc001ggz.3_Missense_Mutation_p.R53C|GORAB_uc009wvx.2_Translation_Start_Site|GORAB_uc001ghb.2_Translation_Start_Site|GORAB_uc001ghc.2_Translation_Start_Site	NM_152281	NP_689494	Q5T7V8	GORAB_HUMAN	golgin, RAB6-interacting isoform a	53						Golgi apparatus|nucleus					0																		---	---	---	---
FMO3	2328	broad.mit.edu	37	1	171073005	171073005	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171073005A>T	uc001ghi.2	+	3	323	c.212A>T	c.(211-213)GAC>GTC	p.D71V	FMO3_uc001ghh.2_Missense_Mutation_p.D71V|FMO3_uc010pmb.1_Missense_Mutation_p.D51V|FMO3_uc010pmc.1_Intron|MIR1295_hsa-mir-1295|MI0006357_5'Flank	NM_001002294	NP_001002294	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	71					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)																	---	---	---	---
C1orf9	51430	broad.mit.edu	37	1	172547526	172547526	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172547526T>G	uc001giq.3	+	14	1745	c.1429T>G	c.(1429-1431)TAT>GAT	p.Y477D	C1orf9_uc010pmm.1_Missense_Mutation_p.Y477D|C1orf9_uc009wwd.2_Missense_Mutation_p.Y433D|C1orf9_uc010pmn.1_Missense_Mutation_p.Y440D|C1orf9_uc010pmo.1_RNA	NM_014283	NP_055098	Q9UBS9	OSPT_HUMAN	chromosome 1 open reading frame 9 protein	477					multicellular organismal development|ossification	integral to membrane|rough endoplasmic reticulum membrane				ovary(2)	2		Breast(1374;0.212)		Colorectal(1306;3.98e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00544)														---	---	---	---
KLHL20	27252	broad.mit.edu	37	1	173703342	173703342	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173703342G>A	uc001gjc.2	+	3	693	c.514G>A	c.(514-516)GGC>AGC	p.G172S	KLHL20_uc010pmr.1_Intron|KLHL20_uc009wwf.2_Missense_Mutation_p.G154S|KLHL20_uc001gjd.2_Missense_Mutation_p.G172S	NM_014458	NP_055273	Q9Y2M5	KLH20_HUMAN	kelch-like 20	172	BACK.				cytoskeleton organization|negative regulation of apoptosis|proteasomal ubiquitin-dependent protein catabolic process|response to interferon-alpha	actin cytoskeleton|cell surface|Cul3-RING ubiquitin ligase complex|Golgi apparatus|perinuclear region of cytoplasm|PML body	actin binding|interferon-gamma binding|ubiquitin-protein ligase activity			ovary(1)	1																		---	---	---	---
CACYBP	27101	broad.mit.edu	37	1	174979173	174979173	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174979173G>A	uc001gkj.1	+	6	1070	c.645G>A	c.(643-645)GTG>GTA	p.V215V	CACYBP_uc001gki.1_Silent_p.V172V	NM_014412	NP_055227	Q9HB71	CYBP_HUMAN	calcyclin binding protein isoform 1	215	SGS.|Interaction with S100A6 (By similarity).|Interaction with SKP1.					beta-catenin destruction complex	protein homodimerization activity				0																		---	---	---	---
TNN	63923	broad.mit.edu	37	1	175063176	175063176	+	Missense_Mutation	SNP	G	A	A	rs143661378		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175063176G>A	uc001gkl.1	+	7	1488	c.1375G>A	c.(1375-1377)GCA>ACA	p.A459T	TNN_uc010pmx.1_Missense_Mutation_p.A459T	NM_022093	NP_071376	Q9UQP3	TENN_HUMAN	tenascin N precursor	459	Fibronectin type-III 3.				cell growth|cell migration|signal transduction	extracellular space|proteinaceous extracellular matrix				large_intestine(5)|ovary(3)|central_nervous_system(1)	9		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)														---	---	---	---
PAPPA2	60676	broad.mit.edu	37	1	176564594	176564594	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176564594C>T	uc001gkz.2	+	3	3018	c.1854C>T	c.(1852-1854)TGC>TGT	p.C618C	PAPPA2_uc001gky.1_Silent_p.C618C|PAPPA2_uc009www.2_RNA	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1	618	Metalloprotease.				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																		---	---	---	---
SOAT1	6646	broad.mit.edu	37	1	179304782	179304782	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179304782C>A	uc001gml.2	+	4	382	c.319C>A	c.(319-321)CAT>AAT	p.H107N	SOAT1_uc010pni.1_Missense_Mutation_p.H42N|SOAT1_uc001gmm.2_Missense_Mutation_p.H49N|SOAT1_uc010pnj.1_5'UTR|SOAT1_uc010pnk.1_Missense_Mutation_p.H42N	NM_003101	NP_003092	P35610	SOAT1_HUMAN	sterol O-acyltransferase 1	107					cholesterol efflux|cholesterol esterification|cholesterol homeostasis|cholesterol metabolic process|cholesterol storage|macrophage derived foam cell differentiation|positive regulation of amyloid precursor protein biosynthetic process|very-low-density lipoprotein particle assembly	endoplasmic reticulum membrane|integral to membrane|microsome	cholesterol binding|cholesterol O-acyltransferase activity|fatty-acyl-CoA binding			central_nervous_system(1)|skin(1)	2					Ezetimibe(DB00973)|Hesperetin(DB01094)													---	---	---	---
CACNA1E	777	broad.mit.edu	37	1	181708322	181708322	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181708322T>G	uc001gow.2	+	25	3817	c.3652T>G	c.(3652-3654)TTC>GTC	p.F1218V	CACNA1E_uc009wxs.2_Missense_Mutation_p.F1106V|CACNA1E_uc001gox.1_Missense_Mutation_p.F444V|CACNA1E_uc009wxt.2_Missense_Mutation_p.F444V	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,	1218	III.|Helical; Name=S3 of repeat 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																		---	---	---	---
RNASEL	6041	broad.mit.edu	37	1	182555130	182555130	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182555130C>G	uc001gpj.1	-	1	979	c.812G>C	c.(811-813)AGT>ACT	p.S271T	RNASEL_uc009wxz.1_Missense_Mutation_p.S271T|RNASEL_uc001gpk.2_Missense_Mutation_p.S271T|RNASEL_uc009wya.1_Missense_Mutation_p.S271T	NM_021133	NP_066956	Q05823	RN5A_HUMAN	ribonuclease L	271	2-5A binding (P-loop) 2.				mRNA processing|response to virus|type I interferon-mediated signaling pathway	mitochondrion	ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|metal ion binding|protein kinase activity|RNA binding			ovary(4)|stomach(1)	5														Hereditary_Prostate_Cancer				---	---	---	---
LAMC2	3918	broad.mit.edu	37	1	183196783	183196783	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183196783G>A	uc001gqa.2	+	10	1733	c.1419G>A	c.(1417-1419)ATG>ATA	p.M473I	LAMC2_uc001gpz.3_Missense_Mutation_p.M473I|LAMC2_uc010poa.1_Missense_Mutation_p.M173I	NM_005562	NP_005553	Q13753	LAMC2_HUMAN	laminin, gamma 2 isoform a precursor	473	Laminin EGF-like 6.			M -> I (in Ref. 1; CAA78728/CAA78729).	cell adhesion|epidermis development|hemidesmosome assembly		heparin binding			skin(2)|ovary(1)	3																		---	---	---	---
SMG7	9887	broad.mit.edu	37	1	183511600	183511600	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183511600A>C	uc001gqg.2	+	14	1927	c.1805A>C	c.(1804-1806)AAG>ACG	p.K602T	SMG7_uc010pob.1_Intron|SMG7_uc001gqf.2_Intron|SMG7_uc001gqh.2_Intron|SMG7_uc001gqi.2_Intron|SMG7_uc010poc.1_Missense_Mutation_p.K560T	NM_173156	NP_775179	Q92540	SMG7_HUMAN	SMG-7 homolog isoform 1	602					mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation	cytoplasm|intermediate filament cytoskeleton|nucleus	protein phosphatase 2A binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	186094772	186094772	+	Missense_Mutation	SNP	C	T	T	rs147851396	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186094772C>T	uc001grq.1	+	82	12765	c.12536C>T	c.(12535-12537)ACG>ATG	p.T4179M	HMCN1_uc001grs.1_5'Flank	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	4179	Ig-like C2-type 41.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
TPR	7175	broad.mit.edu	37	1	186321115	186321115	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186321115G>A	uc001grv.2	-	19	2759	c.2462C>T	c.(2461-2463)ACA>ATA	p.T821I		NM_003292	NP_003283	P12270	TPR_HUMAN	nuclear pore complex-associated protein TPR	821	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								---	---	---	---
CDC73	79577	broad.mit.edu	37	1	193091328	193091328	+	5'UTR	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193091328A>G	uc001gtb.2	+	1						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		OREG0014058	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CFH	3075	broad.mit.edu	37	1	196716298	196716298	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196716298C>T	uc001gtj.3	+	22	3791	c.3551C>T	c.(3550-3552)ACA>ATA	p.T1184I		NM_000186	NP_000177	P08603	CFAH_HUMAN	complement factor H isoform a precursor	1184	Sushi 20.		T -> R (in CFH deficiency).		complement activation, alternative pathway	extracellular space				skin(4)|ovary(1)|breast(1)	6																		---	---	---	---
CRB1	23418	broad.mit.edu	37	1	197404381	197404381	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197404381A>G	uc001gtz.2	+	9	3523	c.3388A>G	c.(3388-3390)ACC>GCC	p.T1130A	CRB1_uc010poz.1_Missense_Mutation_p.T1106A|CRB1_uc010ppa.1_RNA|CRB1_uc009wza.2_Missense_Mutation_p.T1018A|CRB1_uc010ppb.1_Intron|CRB1_uc010ppd.1_Missense_Mutation_p.T611A|CRB1_uc001gub.1_Missense_Mutation_p.T779A	NM_201253	NP_957705	P82279	CRUM1_HUMAN	crumbs homolog 1 precursor	1130	Extracellular (Potential).|Laminin G-like 3.				cell-cell signaling|establishment or maintenance of cell polarity	apical plasma membrane|extracellular region|integral to membrane	calcium ion binding|protein binding			ovary(5)|skin(3)|large_intestine(1)	9																		---	---	---	---
KIF14	9928	broad.mit.edu	37	1	200561226	200561226	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200561226A>T	uc010ppk.1	-	16	3234	c.2795T>A	c.(2794-2796)CTC>CAC	p.L932H	KIF14_uc010ppj.1_Missense_Mutation_p.L441H	NM_014875	NP_055690	Q15058	KIF14_HUMAN	kinesin family member 14	932	Potential.|Required for CIT-binding.				microtubule-based movement	cytoplasm|microtubule|nucleus|spindle	ATP binding|microtubule motor activity|protein binding			breast(3)|ovary(2)|skin(2)	7																		---	---	---	---
ELF3	1999	broad.mit.edu	37	1	201982153	201982153	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201982153T>G	uc001gxg.3	+	5	3869	c.677T>G	c.(676-678)CTC>CGC	p.L226R	ELF3_uc001gxi.3_Missense_Mutation_p.L226R|ELF3_uc001gxh.3_Missense_Mutation_p.L226R	NM_004433	NP_004424	P78545	ELF3_HUMAN	E74-like factor 3 (ets domain transcription	226					epidermis development|epithelial cell differentiation|inflammatory response|mammary gland involution|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	Golgi apparatus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity				0																		---	---	---	---
PPP1R12B	4660	broad.mit.edu	37	1	202403879	202403879	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202403879G>A	uc001gya.1	+	9	1381	c.1237G>A	c.(1237-1239)GCC>ACC	p.A413T	PPP1R12B_uc001gxy.2_Missense_Mutation_p.A413T|PPP1R12B_uc009xad.1_Missense_Mutation_p.A219T|PPP1R12B_uc009xae.1_Intron|PPP1R12B_uc001gxz.1_Missense_Mutation_p.A413T	NM_002481	NP_002472	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory (inhibitor)	413					regulation of muscle contraction|signal transduction	cytoplasm	enzyme activator activity			ovary(3)	3			BRCA - Breast invasive adenocarcinoma(75;0.166)															---	---	---	---
NFASC	23114	broad.mit.edu	37	1	204953228	204953228	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204953228C>T	uc001hbj.2	+						NFASC_uc010pra.1_Silent_p.R844R|NFASC_uc001hbi.2_Silent_p.R844R|NFASC_uc010prb.1_Silent_p.R859R|NFASC_uc010prc.1_Silent_p.R415R|NFASC_uc001hbk.1_Silent_p.R654R|NFASC_uc001hbl.1_Intron|NFASC_uc001hbm.1_5'Flank	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)															---	---	---	---
SLC41A1	254428	broad.mit.edu	37	1	205766118	205766118	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205766118T>C	uc001hdh.1	-	8	1878	c.1006A>G	c.(1006-1008)ATC>GTC	p.I336V	SLC41A1_uc001hdg.1_5'Flank|uc001hdi.1_5'Flank	NM_173854	NP_776253	Q8IVJ1	S41A1_HUMAN	solute carrier family 41 member 1	336	Helical; (Potential).					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	206611341	206611341	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206611341A>C	uc001hdy.2	+	13	1733	c.1400A>C	c.(1399-1401)AAC>ACC	p.N467T	SRGAP2_uc010prt.1_Missense_Mutation_p.N390T|SRGAP2_uc001hdx.2_Missense_Mutation_p.N467T|SRGAP2_uc010pru.1_Missense_Mutation_p.N390T|SRGAP2_uc010prv.1_Missense_Mutation_p.N391T	NM_015326	NP_056141	O75044	FNBP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2	554	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)																	---	---	---	---
RASSF5	83593	broad.mit.edu	37	1	206711624	206711624	+	Splice_Site	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206711624T>C	uc001hed.2	+	2	636	c.579_splice	c.e2+2	p.Q193_splice	RASSF5_uc001hec.1_Splice_Site_p.Q193_splice|RASSF5_uc001hee.2_Splice_Site_p.Q193_splice	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)															---	---	---	---
DYRK3	8444	broad.mit.edu	37	1	206821020	206821020	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206821020A>G	uc001hej.2	+	3	645	c.477A>G	c.(475-477)AAA>AAG	p.K159K	DYRK3_uc001hek.2_Intron|DYRK3_uc001hei.2_Silent_p.K139K	NM_003582	NP_003573	O43781	DYRK3_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation	159					erythrocyte differentiation	nucleus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			stomach(2)|central_nervous_system(1)	3	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)															---	---	---	---
DYRK3	8444	broad.mit.edu	37	1	206821627	206821627	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206821627G>A	uc001hej.2	+	3	1252	c.1084G>A	c.(1084-1086)GAG>AAG	p.E362K	DYRK3_uc001hek.2_Intron|DYRK3_uc001hei.2_Missense_Mutation_p.E342K	NM_003582	NP_003573	O43781	DYRK3_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation	362	Protein kinase.				erythrocyte differentiation	nucleus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			stomach(2)|central_nervous_system(1)	3	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)															---	---	---	---
PFKFB2	5208	broad.mit.edu	37	1	207235391	207235391	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207235391G>A	uc001hfg.2	+	3	288	c.179G>A	c.(178-180)CGC>CAC	p.R60H	PFKFB2_uc010psc.1_5'UTR|PFKFB2_uc001hfh.2_Missense_Mutation_p.R60H|PFKFB2_uc009xcc.2_Missense_Mutation_p.R18H|PFKFB2_uc010psd.1_5'Flank	NM_006212	NP_006203	O60825	F262_HUMAN	6-phosphofructo-2-kinase/fructose-2,	60	6-phosphofructo-2-kinase.				fructose 2,6-bisphosphate metabolic process|glycolysis	cytosol	6-phosphofructo-2-kinase activity|ATP binding|fructose-2,6-bisphosphate 2-phosphatase activity			ovary(1)	1	Prostate(682;0.19)																	---	---	---	---
PLXNA2	5362	broad.mit.edu	37	1	208390973	208390973	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208390973T>C	uc001hgz.2	-	2	1053	c.295A>G	c.(295-297)ATC>GTC	p.I99V	PLXNA2_uc001hha.3_Missense_Mutation_p.I153V	NM_025179	NP_079455	O75051	PLXA2_HUMAN	plexin A2 precursor	99	Extracellular (Potential).|Sema.				axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)|central_nervous_system(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.199)														---	---	---	---
USH2A	7399	broad.mit.edu	37	1	216040460	216040460	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216040460G>A	uc001hku.1	-	44	9121	c.8734C>T	c.(8734-8736)CCG>TCG	p.P2912S		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	2912	Extracellular (Potential).|Fibronectin type-III 15.				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)			---	---	---	---
RRP15	51018	broad.mit.edu	37	1	218458762	218458762	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218458762T>C	uc001hlj.2	+	1	134	c.104T>C	c.(103-105)CTG>CCG	p.L35P		NM_016052	NP_057136	Q9Y3B9	RRP15_HUMAN	ribosomal RNA processing 15 homolog	35						mitochondrion|nucleolus	protein binding				0				all cancers(67;0.0315)|OV - Ovarian serous cystadenocarcinoma(81;0.0411)|GBM - Glioblastoma multiforme(131;0.06)|Epithelial(68;0.248)														---	---	---	---
EPRS	2058	broad.mit.edu	37	1	220146681	220146681	+	Silent	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220146681G>T	uc001hly.1	-	29	4413	c.4143C>A	c.(4141-4143)GCC>GCA	p.A1381A		NM_004446	NP_004437	P07814	SYEP_HUMAN	glutamyl-prolyl tRNA synthetase	1381	Prolyl-tRNA synthetase.				glutamyl-tRNA aminoacylation|prolyl-tRNA aminoacylation|protein complex assembly	cytosol|soluble fraction	ATP binding|glutamate-tRNA ligase activity|proline-tRNA ligase activity|protein binding|RNA binding			ovary(1)|skin(1)	2				GBM - Glioblastoma multiforme(131;0.0735)	L-Glutamic Acid(DB00142)|L-Proline(DB00172)													---	---	---	---
RAB3GAP2	25782	broad.mit.edu	37	1	220345998	220345998	+	Silent	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220345998G>T	uc010puk.1	-	22	2561	c.2397C>A	c.(2395-2397)TCC>TCA	p.S799S	RAB3GAP2_uc001hmf.2_RNA|RAB3GAP2_uc001hmg.2_Silent_p.S379S	NM_012414	NP_036546	Q9H2M9	RBGPR_HUMAN	rab3 GTPase-activating protein, non-catalytic	799					intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(131;0.0443)														---	---	---	---
TLR5	7100	broad.mit.edu	37	1	223284208	223284208	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223284208T>C	uc001hnv.1	-	4	2612	c.2166A>G	c.(2164-2166)CAA>CAG	p.Q722Q	TLR5_uc001hnw.1_Silent_p.Q722Q	NM_003268	NP_003259	O60602	TLR5_HUMAN	toll-like receptor 5 precursor	722	Cytoplasmic (Potential).|TIR.		Missing (in 10% of the population; abolishes flagellin signaling; associated with resistance to SLEB1).		cellular response to mechanical stimulus|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of interleukin-8 production|positive regulation of toll-like receptor signaling pathway	integral to membrane|plasma membrane	interleukin-1 receptor binding|transmembrane receptor activity			ovary(2)|lung(1)|skin(1)	4				GBM - Glioblastoma multiforme(131;0.0851)														---	---	---	---
PYCR2	29920	broad.mit.edu	37	1	226109606	226109606	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226109606C>A	uc001hpq.2	-	4	647	c.492G>T	c.(490-492)GAG>GAT	p.E164D	LEFTY1_uc010pvj.1_Intron|PYCR2_uc001hpp.2_Missense_Mutation_p.E128D|PYCR2_uc001hpr.2_Missense_Mutation_p.E117D|PYCR2_uc001hps.1_Missense_Mutation_p.E117D	NM_013328	NP_037460	Q96C36	P5CR2_HUMAN	pyrroline-5-carboxylate reductase family, member	164					proline biosynthetic process	cytoplasm	binding|pyrroline-5-carboxylate reductase activity				0	Breast(184;0.197)				L-Proline(DB00172)|NADH(DB00157)													---	---	---	---
LEFTY2	7044	broad.mit.edu	37	1	226125335	226125335	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226125335C>T	uc001hpt.1	-	4	987	c.907G>A	c.(907-909)GCC>ACC	p.A303T	LEFTY2_uc010pvk.1_Missense_Mutation_p.A269T|LEFTY2_uc009xek.1_3'UTR	NM_003240	NP_003231	O00292	LFTY2_HUMAN	endometrial bleeding associated factor	303					cell growth|multicellular organismal development|platelet activation|platelet degranulation|transforming growth factor beta receptor signaling pathway	extracellular space|platelet alpha granule lumen	cytokine activity|growth factor activity|transforming growth factor beta receptor binding				0	Breast(184;0.197)																	---	---	---	---
ITPKB	3707	broad.mit.edu	37	1	226924476	226924476	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226924476C>T	uc010pvo.1	-	2	1024	c.684G>A	c.(682-684)TCG>TCA	p.S228S	ITPKB_uc001hqh.2_Silent_p.S228S	NM_002221	NP_002212	P27987	IP3KB_HUMAN	1D-myo-inositol-trisphosphate 3-kinase B	228							ATP binding|calmodulin binding|inositol trisphosphate 3-kinase activity			ovary(4)|central_nervous_system(1)	5		Prostate(94;0.0773)																---	---	---	---
SIPA1L2	57568	broad.mit.edu	37	1	232539881	232539881	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232539881C>T	uc001hvg.2	-	18	4964	c.4806G>A	c.(4804-4806)ACG>ACA	p.T1602T	SIPA1L2_uc001hvf.2_Intron	NM_020808	NP_065859	Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like	1602					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)																---	---	---	---
LYST	1130	broad.mit.edu	37	1	235878668	235878668	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235878668C>T	uc001hxj.2	-						LYST_uc001hxi.2_Intron	NM_000081	NP_000072			lysosomal trafficking regulator						defense response to bacterium|defense response to protozoan|defense response to virus|endosome to lysosome transport via multivesicular body sorting pathway|leukocyte chemotaxis|mast cell secretory granule organization|melanosome organization|natural killer cell mediated cytotoxicity|protein transport	cytoplasm|microtubule cytoskeleton	protein binding			ovary(6)|breast(4)|central_nervous_system(2)	12	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)											Chediak-Higashi_syndrome				---	---	---	---
ACTN2	88	broad.mit.edu	37	1	236924414	236924414	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236924414G>A	uc001hyf.2	+	20	2671	c.2467G>A	c.(2467-2469)GCT>ACT	p.A823T	ACTN2_uc001hyg.2_Missense_Mutation_p.A615T|ACTN2_uc009xgi.1_Missense_Mutation_p.A823T|ACTN2_uc010pxu.1_Missense_Mutation_p.A512T|ACTN2_uc001hyh.2_Missense_Mutation_p.A511T	NM_001103	NP_001094	P35609	ACTN2_HUMAN	actinin, alpha 2	823	EF-hand 2.				focal adhesion assembly|microspike assembly|muscle filament sliding|platelet activation|platelet degranulation|protein homotetramerization|regulation of apoptosis|synaptic transmission	actin filament|cytosol|dendritic spine|extracellular region|filopodium|focal adhesion|nucleolus|platelet alpha granule lumen|pseudopodium|Z disc	actin binding|calcium ion binding|FATZ 1 binding|identical protein binding|integrin binding|protein dimerization activity|structural constituent of muscle|titin binding|titin Z domain binding|ZASP binding			ovary(4)|skin(1)	5	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)															---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237532852	237532852	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237532852C>T	uc001hyl.1	+	6	448	c.328C>T	c.(328-330)CAT>TAT	p.H110Y		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	110	Cytoplasmic (By similarity).|MIR 1.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)															---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237586442	237586442	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237586442T>C	uc001hyl.1	+	12	1019	c.899T>C	c.(898-900)GTC>GCC	p.V300A		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	300	Cytoplasmic (By similarity).|MIR 4.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)															---	---	---	---
FMN2	56776	broad.mit.edu	37	1	240497463	240497463	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240497463C>T	uc010pyd.1	+	13	4924	c.4699C>T	c.(4699-4701)CAG>TAG	p.Q1567*	FMN2_uc010pye.1_Nonsense_Mutation_p.Q1571*|FMN2_uc010pyf.1_Nonsense_Mutation_p.Q213*|FMN2_uc010pyg.1_Nonsense_Mutation_p.Q163*	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2	1567	FH2.|Potential.				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)															---	---	---	---
ZNF496	84838	broad.mit.edu	37	1	247464264	247464264	+	Missense_Mutation	SNP	C	A	A	rs145725779		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247464264C>A	uc001ico.2	-	9	1786	c.1321G>T	c.(1321-1323)GGG>TGG	p.G441W	ZNF496_uc009xgv.2_Missense_Mutation_p.G477W|ZNF496_uc001icp.2_Missense_Mutation_p.G441W	NM_032752	NP_116141	Q96IT1	ZN496_HUMAN	zinc finger protein 496	441	C2H2-type 2.				positive regulation of transcription, DNA-dependent|viral reproduction		DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_cancers(71;0.000136)|all_epithelial(71;2.62e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)		OV - Ovarian serous cystadenocarcinoma(106;0.00703)															---	---	---	---
OR2T4	127074	broad.mit.edu	37	1	248525618	248525618	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248525618A>C	uc001ieh.1	+	1	736	c.736A>C	c.(736-738)ATT>CTT	p.I246L		NM_001004696	NP_001004696	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T,	246	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)															---	---	---	---
PXDN	7837	broad.mit.edu	37	2	1669992	1669992	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1669992C>T	uc002qxa.2	-	10	1349	c.1285G>A	c.(1285-1287)GTC>ATC	p.V429I	PXDN_uc002qxb.1_Missense_Mutation_p.V429I|PXDN_uc002qxc.1_Missense_Mutation_p.V246I	NM_012293	NP_036425	Q92626	PXDN_HUMAN	peroxidasin precursor	429					extracellular matrix organization|hydrogen peroxide catabolic process|immune response	endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix	extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity			pancreas(6)|ovary(2)	8	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)														---	---	---	---
RSAD2	91543	broad.mit.edu	37	2	7027252	7027252	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7027252A>T	uc002qyp.1	+	3	831	c.695A>T	c.(694-696)GAC>GTC	p.D232V		NM_080657	NP_542388	Q8WXG1	RSAD2_HUMAN	radical S-adenosyl methionine domain containing	232					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)														---	---	---	---
NOL10	79954	broad.mit.edu	37	2	10811735	10811735	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10811735C>A	uc002raq.2	-	6	534	c.409G>T	c.(409-411)GGG>TGG	p.G137W	NOL10_uc010yje.1_Missense_Mutation_p.G111W|NOL10_uc010yjf.1_Missense_Mutation_p.G87W|NOL10_uc002rap.2_Missense_Mutation_p.G137W|NOL10_uc002rar.2_Intron	NM_024894	NP_079170	Q9BSC4	NOL10_HUMAN	nucleolar protein 10	137						nucleolus					0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.207)														---	---	---	---
LPIN1	23175	broad.mit.edu	37	2	11923966	11923966	+	Silent	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11923966C>A	uc010yjn.1	+	9	1442	c.1168C>A	c.(1168-1170)CGA>AGA	p.R390R	LPIN1_uc010yjm.1_Silent_p.R475R|LPIN1_uc002rbt.2_Silent_p.R390R|LPIN1_uc002rbs.2_Silent_p.R426R	NM_145693	NP_663731	Q14693	LPIN1_HUMAN	lipin 1	390					fatty acid catabolic process|transcription, DNA-dependent|triglyceride biosynthetic process|triglyceride mobilization	cytosol|endoplasmic reticulum membrane	phosphatidate phosphatase activity			ovary(2)|large_intestine(1)|skin(1)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)														---	---	---	---
MYCN	4613	broad.mit.edu	37	2	16086094	16086094	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16086094A>G	uc002rci.2	+	3	1570	c.1270A>G	c.(1270-1272)AAA>GAA	p.K424E	MYCN_uc010yjr.1_Missense_Mutation_p.K416E	NM_005378	NP_005369	P04198	MYCN_HUMAN	v-myc myelocytomatosis viral related oncogene,	424	Helix-loop-helix motif.				regulation of transcription from RNA polymerase II promoter	chromatin|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	5	all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(3;0.000332)					A		neuroblastoma								---	---	---	---
RAD51AP2	729475	broad.mit.edu	37	2	17698672	17698672	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17698672T>C	uc002rcl.1	-	1	1035	c.1011A>G	c.(1009-1011)CAA>CAG	p.Q337Q	RAD51AP2_uc010exn.1_Silent_p.Q328Q	NM_001099218	NP_001092688	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	337										ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)																	---	---	---	---
WDR35	57539	broad.mit.edu	37	2	20145536	20145536	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20145536C>T	uc002rdi.2	-						WDR35_uc002rdj.2_Intron|WDR35_uc010ext.2_Intron|WDR35_uc002rdh.2_Intron|WDR35_uc002rdk.3_Intron	NM_001006657	NP_001006658			WD repeat domain 35 isoform 1											ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
APOB	338	broad.mit.edu	37	2	21235151	21235151	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21235151G>C	uc002red.2	-	26	4717	c.4589C>G	c.(4588-4590)ACC>AGC	p.T1530S		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	1530					cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			ovary(11)|skin(9)|central_nervous_system(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)	27	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)													---	---	---	---
MFSD2B	388931	broad.mit.edu	37	2	24240374	24240374	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24240374C>T	uc002reo.1	+	6	611	c.597C>T	c.(595-597)CAC>CAT	p.H199H	MFSD2B_uc010exz.1_RNA	NM_001080473	NP_001073942	A6NFX1	MFS2B_HUMAN	major facilitator superfamily domain containing	199	Helical; (Potential).				transport	integral to membrane				ovary(2)	2																		---	---	---	---
OTOF	9381	broad.mit.edu	37	2	26697430	26697430	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26697430C>A	uc002rhk.2	-	26	3366	c.3239G>T	c.(3238-3240)CGT>CTT	p.R1080L	OTOF_uc010yla.1_5'Flank|OTOF_uc002rhh.2_Missense_Mutation_p.R333L|OTOF_uc002rhi.2_Missense_Mutation_p.R390L|OTOF_uc002rhj.2_Missense_Mutation_p.R333L	NM_194248	NP_919224	Q9HC10	OTOF_HUMAN	otoferlin isoform a	1080	Cytoplasmic (Potential).				cellular membrane fusion|sensory perception of sound|synaptic vesicle exocytosis	basolateral plasma membrane|cell junction|cytosol|endoplasmic reticulum membrane|integral to membrane|membrane fraction|synaptic vesicle membrane	calcium ion binding			ovary(3)|breast(2)|central_nervous_system(1)|pancreas(1)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
TMEM214	54867	broad.mit.edu	37	2	27259942	27259942	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27259942C>T	uc002ria.3	+						TMEM214_uc010yle.1_Intron|TMEM214_uc002rib.3_Intron	NM_017727	NP_060197			transmembrane protein 214 isoform 1							integral to membrane	protein binding				0																		---	---	---	---
SNX17	9784	broad.mit.edu	37	2	27599537	27599537	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27599537A>G	uc002rkg.1	+	15	1586	c.1364A>G	c.(1363-1365)GAT>GGT	p.D455G	SNX17_uc010ylj.1_Missense_Mutation_p.D435G|SNX17_uc010ylk.1_Missense_Mutation_p.D241G|SNX17_uc010eza.1_Missense_Mutation_p.D241G|SNX17_uc002rki.1_RNA|SNX17_uc002rkh.1_Missense_Mutation_p.D241G|SNX17_uc010yll.1_Missense_Mutation_p.D241G|SNX17_uc010ylm.1_Missense_Mutation_p.D241G|SNX17_uc010yln.1_Missense_Mutation_p.D443G|SNX17_uc010ylo.1_Missense_Mutation_p.D373G|SNX17_uc010ylp.1_Missense_Mutation_p.D430G|SNX17_uc010ylq.1_Missense_Mutation_p.D241G	NM_014748	NP_055563	Q15036	SNX17_HUMAN	sorting nexin 17	455					cell communication|endosome transport|intracellular protein transport|regulation of endocytosis|signal transduction	cytoplasmic vesicle membrane|cytosol|early endosome|Golgi apparatus	low-density lipoprotein particle receptor binding|phosphatidylinositol binding|protein C-terminus binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
PPM1G	5496	broad.mit.edu	37	2	27607655	27607655	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27607655G>A	uc002rkl.2	-	6	817	c.710C>T	c.(709-711)GCT>GTT	p.A237V	PPM1G_uc002rkm.2_Intron	NM_002707	NP_002698	O15355	PPM1G_HUMAN	protein phosphatase 1G	237					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)																	---	---	---	---
GCKR	2646	broad.mit.edu	37	2	27745463	27745463	+	Splice_Site	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27745463T>C	uc002rky.2	+	18	1773	c.1707_splice	c.e18+2	p.Q569_splice	GCKR_uc010ezd.2_Splice_Site_p.Q567_splice|GCKR_uc010ylu.1_Splice_Site_p.Q379_splice	NM_001486	NP_001477			glucokinase regulatory protein						carbohydrate metabolic process|glucose transport|negative regulation of glucokinase activity|positive regulation of gene expression|protein import into nucleus, translocation|regulation of glucose transport|response to fructose stimulus|transmembrane transport|triglyceride homeostasis|urate metabolic process	cytosol|nucleoplasm	fructose-6-phosphate binding|protein binding			ovary(2)	2	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
SLC4A1AP	22950	broad.mit.edu	37	2	27890198	27890198	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27890198G>T	uc002rlk.3	+	3	1367	c.1085G>T	c.(1084-1086)AGG>ATG	p.R362M		NM_018158	NP_060628	Q9BWU0	NADAP_HUMAN	solute carrier family 4 (anion exchanger),	362						cytoplasm|nucleus	double-stranded RNA binding|protein binding				0	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
PLB1	151056	broad.mit.edu	37	2	28821528	28821528	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28821528G>T	uc002rmb.1	+	35	2375	c.2375G>T	c.(2374-2376)CGG>CTG	p.R792L	PLB1_uc010ezj.1_Missense_Mutation_p.R781L	NM_153021	NP_694566	Q6P1J6	PLB1_HUMAN	phospholipase B1 precursor	792	4 X 308-326 AA approximate repeats.|Extracellular (Potential).|3.				lipid catabolic process|retinoid metabolic process|steroid metabolic process	apical plasma membrane|integral to membrane	lysophospholipase activity|phospholipase A2 activity|retinyl-palmitate esterase activity			ovary(4)|large_intestine(2)|skin(2)|breast(1)	9	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
FAM179A	165186	broad.mit.edu	37	2	29225485	29225485	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29225485G>A	uc010ezl.2	+	5	862	c.511G>A	c.(511-513)GTG>ATG	p.V171M	FAM179A_uc010ymm.1_Missense_Mutation_p.V171M	NM_199280	NP_954974	Q6ZUX3	F179A_HUMAN	hypothetical protein LOC165186	171							binding			ovary(3)|skin(1)	4																		---	---	---	---
C2orf71	388939	broad.mit.edu	37	2	29297016	29297016	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29297016T>C	uc002rmt.1	-	1	112	c.112A>G	c.(112-114)AGA>GGA	p.R38G		NM_001029883	NP_001025054	A6NGG8	CB071_HUMAN	hypothetical protein LOC388939	38					response to stimulus|visual perception	photoreceptor outer segment				skin(1)	1																		---	---	---	---
ALK	238	broad.mit.edu	37	2	29416374	29416374	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29416374G>A	uc002rmy.2	-	29	5486	c.4579C>T	c.(4579-4581)CCA>TCA	p.P1527S	ALK_uc010ymo.1_Missense_Mutation_p.P459S	NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor	1527	Cytoplasmic (Potential).				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				---	---	---	---
LBH	81606	broad.mit.edu	37	2	30480448	30480448	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30480448T>C	uc002rne.2	+	3	487	c.279T>C	c.(277-279)GAT>GAC	p.D93D		NM_030915	NP_112177	Q53QV2	LBH_HUMAN	limb bud and heart development homolog	93					multicellular organismal development|transcription, DNA-dependent	cytoplasm|nucleolus					0	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
NLRC4	58484	broad.mit.edu	37	2	32477706	32477706	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32477706A>G	uc002roi.2	-	3	290	c.44T>C	c.(43-45)ATG>ACG	p.M15T	NLRC4_uc002roj.1_Missense_Mutation_p.M15T|NLRC4_uc010ezt.1_Missense_Mutation_p.M15T	NM_021209	NP_067032	Q9NPP4	NLRC4_HUMAN	caspase recruitment domain protein 12	15	LRR 1.|CARD.				activation of caspase activity|defense response to bacterium|detection of bacterium|interleukin-1 beta secretion|positive regulation of apoptosis	cytoplasm	ATP binding|magnesium ion binding|protein homodimerization activity			ovary(3)|large_intestine(1)|lung(1)|skin(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)																	---	---	---	---
C2orf56	55471	broad.mit.edu	37	2	37473230	37473230	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37473230T>C	uc002rqa.3	+	8	903	c.828T>C	c.(826-828)CCT>CCC	p.P276P	C2orf56_uc010ynj.1_RNA|C2orf56_uc002rqc.3_Silent_p.P178P|C2orf56_uc010ynk.1_Silent_p.P205P|C2orf56_uc010ynl.1_Silent_p.P249P|C2orf56_uc010fah.2_RNA	NM_144736	NP_653337	Q7L592	MIDA_HUMAN	hypothetical protein LOC55471 isoform 1	276					mitochondrial respiratory chain complex I assembly	mitochondrion	enzyme binding|methyltransferase activity			central_nervous_system(1)	1		all_hematologic(82;0.21)																---	---	---	---
CYP1B1	1545	broad.mit.edu	37	2	38301545	38301545	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38301545G>A	uc002rqo.2	-	3	1390	c.987C>T	c.(985-987)GGC>GGT	p.G329G		NM_000104	NP_000095	Q16678	CP1B1_HUMAN	cytochrome P450, family 1, subfamily B,	329					visual perception|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding|protein binding			ovary(1)|central_nervous_system(1)	2		all_hematologic(82;0.21)			Estrone(DB00655)													---	---	---	---
MAP4K3	8491	broad.mit.edu	37	2	39542483	39542483	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39542483A>G	uc002rro.2	-	13	1056	c.965T>C	c.(964-966)GTG>GCG	p.V322A	MAP4K3_uc002rrp.2_Missense_Mutation_p.V322A|MAP4K3_uc010yns.1_5'UTR	NM_003618	NP_003609	Q8IVH8	M4K3_HUMAN	mitogen-activated protein kinase kinase kinase	322					JNK cascade		ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(3)|lung(3)|stomach(1)|pancreas(1)	8		all_hematologic(82;0.211)																---	---	---	---
SLC8A1	6546	broad.mit.edu	37	2	40657409	40657409	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40657409C>T	uc002rrx.2	-	1	36	c.12G>A	c.(10-12)ATG>ATA	p.M4I	SLC8A1_uc002rry.2_Missense_Mutation_p.M4I|SLC8A1_uc002rrz.2_Missense_Mutation_p.M4I|SLC8A1_uc002rsa.2_Missense_Mutation_p.M4I|SLC8A1_uc002rsd.3_Missense_Mutation_p.M4I|SLC8A1_uc002rsb.1_Missense_Mutation_p.M4I|SLC8A1_uc010fan.1_Missense_Mutation_p.M4I|SLC8A1_uc002rsc.1_Missense_Mutation_p.M4I	NM_021097	NP_066920	P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium	4					cell communication|muscle contraction|platelet activation	integral to plasma membrane	calcium:sodium antiporter activity|calmodulin binding|heat shock protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)													---	---	---	---
PKDCC	91461	broad.mit.edu	37	2	42284780	42284780	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42284780A>G	uc002rsg.2	+	7	1613	c.1434A>G	c.(1432-1434)CAA>CAG	p.Q478Q		NM_138370	NP_612379	Q504Y2	PKDCC_HUMAN	protein kinase-like protein SgK493	478	Protein kinase.				cell differentiation|embryonic digestive tract development|lung alveolus development|negative regulation of Golgi to plasma membrane protein transport|ossification|palate development|positive regulation of bone mineralization|positive regulation of chondrocyte differentiation|protein transport	Golgi apparatus	ATP binding|protein kinase activity			breast(1)	1																		---	---	---	---
PLEKHH2	130271	broad.mit.edu	37	2	43956786	43956786	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43956786T>C	uc010yny.1	+	18	2815	c.2732T>C	c.(2731-2733)CTT>CCT	p.L911P	PLEKHH2_uc002rtf.3_Missense_Mutation_p.L910P	NM_172069	NP_742066	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H	911	PH 2.					cytoplasm|cytoskeleton|integral to membrane	binding			skin(2)|central_nervous_system(1)	3		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)																---	---	---	---
ABCG8	64241	broad.mit.edu	37	2	44101062	44101062	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44101062G>A	uc002rtq.2	+	9	1438	c.1348G>A	c.(1348-1350)GCC>ACC	p.A450T	ABCG8_uc010yoa.1_Missense_Mutation_p.A449T	NM_022437	NP_071882	Q9H221	ABCG8_HUMAN	ATP-binding cassette sub-family G member 8	450	Helical; Name=2; (Potential).|ABC transmembrane type-2.				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)																---	---	---	---
PRKCE	5581	broad.mit.edu	37	2	46313408	46313408	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46313408G>A	uc002rut.2	+	11	1696	c.1499G>A	c.(1498-1500)CGC>CAC	p.R500H		NM_005400	NP_005391	Q02156	KPCE_HUMAN	protein kinase C, epsilon	500	Protein kinase.				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)															---	---	---	---
PSME4	23198	broad.mit.edu	37	2	54148253	54148253	+	Intron	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54148253G>A	uc002rxp.2	-						PSME4_uc010yop.1_Intron|PSME4_uc010yoq.1_Intron|PSME4_uc010fbu.1_Intron|PSME4_uc010fbv.1_Intron	NM_014614	NP_055429			proteasome (prosome, macropain) activator						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|multicellular organismal development|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|spermatogenesis|viral reproduction	nuclear speck|proteasome complex	binding			ovary(2)|breast(2)|pancreas(1)	5			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)															---	---	---	---
SPTBN1	6711	broad.mit.edu	37	2	54856186	54856186	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54856186C>T	uc002rxu.2	+	14	2164	c.1915C>T	c.(1915-1917)CGC>TGC	p.R639C	SPTBN1_uc002rxv.1_Missense_Mutation_p.R639C|SPTBN1_uc002rxx.2_Missense_Mutation_p.R626C	NM_003128	NP_003119	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1 isoform 1	639	Spectrin 4.				actin filament capping|axon guidance	cytosol|nucleolus|plasma membrane|sarcomere|spectrin	actin binding|calmodulin binding|protein binding|structural constituent of cytoskeleton			ovary(3)|breast(2)|central_nervous_system(2)|skin(1)	8			Lung(47;0.24)															---	---	---	---
MTIF2	4528	broad.mit.edu	37	2	55470172	55470172	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55470172T>G	uc002ryn.2	-	14	2346	c.1609A>C	c.(1609-1611)ACC>CCC	p.T537P	MTIF2_uc010yox.1_Missense_Mutation_p.T206P|MTIF2_uc002ryo.2_Missense_Mutation_p.T537P	NM_001005369	NP_001005369	P46199	IF2M_HUMAN	mitochondrial translational initiation factor 2	537					regulation of translational initiation	mitochondrion	GTP binding|GTPase activity|ribosomal small subunit binding|translation initiation factor activity			ovary(1)	1																		---	---	---	---
CCDC104	112942	broad.mit.edu	37	2	55762904	55762904	+	Intron	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55762904C>A	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)															---	---	---	---
PNPT1	87178	broad.mit.edu	37	2	55882036	55882036	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55882036T>C	uc002rzf.2	-	18	1547	c.1494A>G	c.(1492-1494)TCA>TCG	p.S498S	PNPT1_uc002rzg.2_RNA	NM_033109	NP_149100	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1	498					mRNA catabolic process|RNA processing	plasma membrane	3'-5'-exoribonuclease activity|polyribonucleotide nucleotidyltransferase activity|RNA binding				0			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)															---	---	---	---
PNPT1	87178	broad.mit.edu	37	2	55914781	55914781	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55914781T>C	uc002rzf.2	-	2	274	c.221A>G	c.(220-222)CAG>CGG	p.Q74R	PNPT1_uc002rzg.2_RNA	NM_033109	NP_149100	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1	74					mRNA catabolic process|RNA processing	plasma membrane	3'-5'-exoribonuclease activity|polyribonucleotide nucleotidyltransferase activity|RNA binding				0			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)															---	---	---	---
KIAA1841	84542	broad.mit.edu	37	2	61343215	61343215	+	Intron	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61343215A>G	uc002saw.3	+						KIAA1841_uc002sax.3_Intron|KIAA1841_uc002say.2_Intron	NM_001129993	NP_001123465			KIAA1841 protein isoform a												0			Epithelial(17;0.193)															---	---	---	---
VPS54	51542	broad.mit.edu	37	2	64176284	64176284	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64176284G>A	uc002scq.2	-	8	1187	c.1024C>T	c.(1024-1026)CAG>TAG	p.Q342*	VPS54_uc002scp.2_Nonsense_Mutation_p.Q330*|VPS54_uc010fct.2_Nonsense_Mutation_p.Q225*	NM_016516	NP_057600	Q9P1Q0	VPS54_HUMAN	vacuolar protein sorting 54 isoform 1	342					protein transport|retrograde transport, endosome to Golgi						0																		---	---	---	---
GFPT1	2673	broad.mit.edu	37	2	69590673	69590673	+	Intron	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69590673A>G	uc002sfh.2	-							NM_002056	NP_002047			glucosamine-fructose-6-phosphate						dolichol-linked oligosaccharide biosynthetic process|energy reserve metabolic process|fructose 6-phosphate metabolic process|glutamine metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol	glutamine-fructose-6-phosphate transaminase (isomerizing) activity|sugar binding			skin(1)	1																		---	---	---	---
RTKN	6242	broad.mit.edu	37	2	74653395	74653395	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74653395C>T	uc002sle.2	-	12	1784	c.1667G>A	c.(1666-1668)CGC>CAC	p.R556H	RTKN_uc002slc.2_Missense_Mutation_p.R543H|RTKN_uc002sld.2_Missense_Mutation_p.R506H	NM_001015055	NP_001015055	Q9BST9	RTKN_HUMAN	rhotekin isoform a	556					apoptosis|regulation of anti-apoptosis|Rho protein signal transduction	intracellular	GTP binding|GTP-Rho binding|GTPase inhibitor activity			skin(1)	1																		---	---	---	---
TMEM150A	129303	broad.mit.edu	37	2	85826422	85826422	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85826422T>C	uc002spw.1	-	7	1314	c.593A>G	c.(592-594)CAT>CGT	p.H198R	TMEM150A_uc002spx.1_Missense_Mutation_p.H114R|TMEM150A_uc002spz.1_Missense_Mutation_p.H145R|TMEM150A_uc002sqa.1_Missense_Mutation_p.H114R|TMEM150A_uc002spy.1_Missense_Mutation_p.H198R	NM_001031738	NP_001026908	Q86TG1	T150A_HUMAN	transmembrane protein 150A isoform 1	198	Helical; (Potential).					integral to membrane|plasma membrane					0																		---	---	---	---
USP39	10713	broad.mit.edu	37	2	85846391	85846391	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85846391C>T	uc002sqe.2	+	2	353	c.317C>T	c.(316-318)CCG>CTG	p.P106L	USP39_uc002sqb.2_5'UTR|USP39_uc010ysu.1_Missense_Mutation_p.P28L|USP39_uc010ysv.1_Missense_Mutation_p.P28L|USP39_uc010fgn.1_Missense_Mutation_p.P106L|USP39_uc002sqf.2_Missense_Mutation_p.P106L|USP39_uc002sqg.2_Missense_Mutation_p.P106L|USP39_uc010fgo.2_Missense_Mutation_p.P106L	NM_006590	NP_006581	Q53GS9	SNUT2_HUMAN	ubiquitin specific protease 39	106					spliceosome assembly|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin thiolesterase activity|zinc ion binding			ovary(1)	1																		---	---	---	---
POLR1A	25885	broad.mit.edu	37	2	86305083	86305083	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86305083G>T	uc002sqs.2	-	11	1658	c.1279C>A	c.(1279-1281)CTG>ATG	p.L427M		NM_015425	NP_056240	O95602	RPA1_HUMAN	DNA-directed RNA polymerase I A	427					termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	DNA-directed RNA polymerase I complex|nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|protein binding|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
POLR1A	25885	broad.mit.edu	37	2	86308010	86308010	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86308010G>A	uc002sqs.2	-	9	1394	c.1015C>T	c.(1015-1017)CGA>TGA	p.R339*	POLR1A_uc002sqv.2_Nonsense_Mutation_p.R339*	NM_015425	NP_056240	O95602	RPA1_HUMAN	DNA-directed RNA polymerase I A	339					termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	DNA-directed RNA polymerase I complex|nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|protein binding|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
SMYD1	150572	broad.mit.edu	37	2	88390545	88390545	+	Silent	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88390545T>G	uc002ssr.2	+	4	545	c.543T>G	c.(541-543)GGT>GGG	p.G181G	SMYD1_uc002ssq.1_Intron|SMYD1_uc002sss.2_5'UTR	NM_198274	NP_938015	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	181	SET.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
GPAT2	150763	broad.mit.edu	37	2	96690519	96690519	+	Splice_Site	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96690519A>G	uc002svf.2	-	14	1651	c.1428_splice	c.e14+1	p.K476_splice	GPAT2_uc002svd.2_Splice_Site_p.K289_splice|GPAT2_uc002sve.2_Splice_Site_p.K278_splice|GPAT2_uc002svg.2_Splice_Site_p.K349_splice|GPAT2_uc010yuh.1_Splice_Site_p.K405_splice|GPAT2_uc002svh.2_Splice_Site_p.K476_splice	NM_207328	NP_997211			glycerol-3-phosphate acyltransferase 2,						glycerol-3-phosphate metabolic process|phospholipid biosynthetic process|triglyceride biosynthetic process	integral to membrane|mitochondrial outer membrane	glycerol-3-phosphate O-acyltransferase activity				0																		---	---	---	---
NCAPH	23397	broad.mit.edu	37	2	97009927	97009927	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97009927T>C	uc002svz.1	+	6	764	c.680T>C	c.(679-681)ATA>ACA	p.I227T	NCAPH_uc010fhu.1_Missense_Mutation_p.I203T|NCAPH_uc010fhv.1_Missense_Mutation_p.I216T|NCAPH_uc010yum.1_Missense_Mutation_p.I203T|NCAPH_uc010fhw.1_Missense_Mutation_p.I216T|NCAPH_uc010yun.1_Missense_Mutation_p.I91T|NCAPH_uc002swa.1_Intron	NM_015341	NP_056156	Q15003	CND2_HUMAN	non-SMC condensin I complex, subunit H	227					cell division|mitotic chromosome condensation	condensin complex|cytoplasm|microtubule cytoskeleton|nucleus				urinary_tract(1)|skin(1)	2		Ovarian(717;0.0221)																---	---	---	---
AFF3	3899	broad.mit.edu	37	2	100368677	100368677	+	Intron	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100368677T>C	uc002tag.2	-						AFF3_uc002taf.2_Intron|AFF3_uc010fiq.1_Intron|AFF3_uc010yvr.1_Intron|AFF3_uc002tah.1_Intron|AFF3_uc010fir.1_Intron	NM_002285	NP_002276			AF4/FMR2 family, member 3 isoform 1						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6																		---	---	---	---
CREG2	200407	broad.mit.edu	37	2	102000137	102000137	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102000137G>T	uc002tba.2	-	2	515	c.469C>A	c.(469-471)CTG>ATG	p.L157M		NM_153836	NP_722578	Q8IUH2	CREG2_HUMAN	cellular repressor of E1A-stimulated genes 2	157						extracellular region	FMN binding			ovary(1)	1																		---	---	---	---
TGFBRAP1	9392	broad.mit.edu	37	2	105885839	105885839	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105885839G>T	uc002tcq.2	-	11	2380	c.2296C>A	c.(2296-2298)CTC>ATC	p.L766I	TGFBRAP1_uc010fjc.2_Missense_Mutation_p.L535I|TGFBRAP1_uc002tcr.3_Missense_Mutation_p.L766I	NM_004257	NP_004248	Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor	766					regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	cytoplasm|membrane	SMAD binding|small GTPase regulator activity|transforming growth factor beta receptor binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
ST6GAL2	84620	broad.mit.edu	37	2	107460018	107460018	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107460018C>A	uc002tdq.2	-	2	535	c.416G>T	c.(415-417)GGG>GTG	p.G139V	ST6GAL2_uc002tdr.2_Missense_Mutation_p.G139V|ST6GAL2_uc002tds.3_Missense_Mutation_p.G139V	NM_001142351	NP_001135823	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide	139	Lumenal (Potential).				growth|multicellular organismal development|oligosaccharide metabolic process|protein glycosylation	Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,6-sialyltransferase activity			pancreas(6)|ovary(4)|skin(1)	11																		---	---	---	---
GCC2	9648	broad.mit.edu	37	2	109116177	109116177	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109116177G>A	uc002tec.2	+	22	5105	c.4951G>A	c.(4951-4953)GAA>AAA	p.E1651K	GCC2_uc002ted.2_Missense_Mutation_p.E1550K	NM_181453	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain-containing 2	1651	Mediates interaction with RAB9A.|GRIP.				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	109371692	109371692	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109371692T>C	uc002tem.3	+	17	2569	c.2443T>C	c.(2443-2445)TGC>CGC	p.C815R		NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2	815					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																		---	---	---	---
POLR1B	84172	broad.mit.edu	37	2	113332994	113332994	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113332994G>T	uc002thw.2	+	15	3676	c.3096G>T	c.(3094-3096)CAG>CAT	p.Q1032H	POLR1B_uc010fkn.2_Missense_Mutation_p.Q976H|POLR1B_uc002thx.2_Missense_Mutation_p.Q893H|POLR1B_uc010fko.2_Missense_Mutation_p.Q849H|POLR1B_uc010fkp.2_Missense_Mutation_p.Q471H|POLR1B_uc010yxn.1_Missense_Mutation_p.Q1070H|POLR1B_uc002thy.2_Missense_Mutation_p.Q893H|POLR1B_uc010yxo.1_Missense_Mutation_p.Q809H	NM_019014	NP_061887	Q9H9Y6	RPA2_HUMAN	RNA polymerase I polypeptide B isoform 1	1032					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																		---	---	---	---
INHBB	3625	broad.mit.edu	37	2	121106699	121106699	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121106699G>A	uc002tmn.2	+	2	519	c.473G>A	c.(472-474)CGC>CAC	p.R158H		NM_002193	NP_002184	P09529	INHBB_HUMAN	inhibin beta B subunit preproprotein	158					activin receptor signaling pathway|cellular response to insulin stimulus|cellular response to starvation|defense response|fat cell differentiation|growth|negative regulation of follicle-stimulating hormone secretion|negative regulation of hepatocyte growth factor biosynthetic process|negative regulation of insulin secretion|ovarian follicle development|positive regulation of follicle-stimulating hormone secretion|positive regulation of ovulation	extracellular region|perinuclear region of cytoplasm	cytokine activity|growth factor activity|hormone activity|host cell surface receptor binding|protein homodimerization activity			pancreas(2)|skin(1)	3		Prostate(154;0.122)																---	---	---	---
GLI2	2736	broad.mit.edu	37	2	121742179	121742179	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121742179C>A	uc010flp.2	+	11	1846	c.1816C>A	c.(1816-1818)CGC>AGC	p.R606S	GLI2_uc002tmq.1_Missense_Mutation_p.R278S|GLI2_uc002tmr.1_Missense_Mutation_p.R261S|GLI2_uc002tmt.3_Missense_Mutation_p.R278S|GLI2_uc002tmu.3_Missense_Mutation_p.R261S|GLI2_uc002tmw.1_Missense_Mutation_p.R589S	NM_005270	NP_005261	P10070	GLI2_HUMAN	GLI-Kruppel family member GLI2	606					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	p.R606L(1)		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	125262029	125262029	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125262029C>T	uc002tno.2	+	8	1584	c.1220C>T	c.(1219-1221)ACA>ATA	p.T407I	CNTNAP5_uc010flu.2_Missense_Mutation_p.T408I	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	407	Laminin G-like 2.|Extracellular (Potential).				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)														---	---	---	---
MAP3K2	10746	broad.mit.edu	37	2	128079763	128079763	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128079763T>C	uc002toj.1	-	11	969	c.904A>G	c.(904-906)AGT>GGT	p.S302G		NM_006609	NP_006600	Q9Y2U5	M3K2_HUMAN	mitogen-activated protein kinase kinase kinase	302					activation of JUN kinase activity|cellular response to mechanical stimulus	nucleus	ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein kinase binding			lung(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	7	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0706)														---	---	---	---
WDR33	55339	broad.mit.edu	37	2	128463932	128463932	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128463932G>A	uc002tpg.1	-	22	4159	c.3976C>T	c.(3976-3978)CGA>TGA	p.R1326*		NM_018383	NP_060853	Q9C0J8	WDR33_HUMAN	WD repeat domain 33 isoform 1	1326					postreplication repair|spermatogenesis	collagen|nucleus	protein binding				0	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)														---	---	---	---
CCDC74B	91409	broad.mit.edu	37	2	130897774	130897774	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130897774G>T	uc002tqm.1	-	5	916	c.854C>A	c.(853-855)ACC>AAC	p.T285N	CCDC74B_uc010yzw.1_Missense_Mutation_p.T387N|CCDC74B_uc002tqn.1_Missense_Mutation_p.T219N	NM_207310	NP_997193	Q96LY2	CC74B_HUMAN	coiled-coil domain containing 74B	285											0	Colorectal(110;0.1)																	---	---	---	---
IMP4	92856	broad.mit.edu	37	2	131103226	131103226	+	Silent	SNP	C	T	T	rs138701816		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131103226C>T	uc002tra.1	+	5	410	c.393C>T	c.(391-393)AAC>AAT	p.N131N		NM_033416	NP_219484	Q96G21	IMP4_HUMAN	IMP4, U3 small nucleolar ribonucleoprotein,	131	Brix.				rRNA processing|translation	nucleolus|ribonucleoprotein complex	aminoacyl-tRNA ligase activity|ATP binding|protein binding			central_nervous_system(2)	2	Colorectal(110;0.1)																	---	---	---	---
CCNT2	905	broad.mit.edu	37	2	135705434	135705434	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135705434A>G	uc002tuc.1	+	7	700	c.668A>G	c.(667-669)TAT>TGT	p.Y223C	CCNT2_uc002tub.1_Missense_Mutation_p.Y223C|CCNT2_uc010zbf.1_Missense_Mutation_p.Y48C|CCNT2_uc002tud.1_Translation_Start_Site	NM_058241	NP_490595	O60583	CCNT2_HUMAN	cyclin T2 isoform b	223					cell cycle|cell division|interspecies interaction between organisms|regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	protein kinase binding			ovary(2)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.107)														---	---	---	---
UBXN4	23190	broad.mit.edu	37	2	136519470	136519470	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136519470C>T	uc002tur.2	+	6	902	c.591C>T	c.(589-591)ATC>ATT	p.I197I	UBXN4_uc002tus.2_Intron	NM_014607	NP_055422	Q92575	UBXN4_HUMAN	UBX domain containing 2	197	Cytoplasmic (Potential).				response to unfolded protein	endoplasmic reticulum membrane|nuclear envelope	protein binding			skin(2)	2																		---	---	---	---
CXCR4	7852	broad.mit.edu	37	2	136872716	136872716	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136872716A>G	uc002tuz.2	-	2	877	c.782T>C	c.(781-783)ATC>ACC	p.I261T	CXCR4_uc002tuy.2_Missense_Mutation_p.I265T|CXCR4_uc010fnk.2_Missense_Mutation_p.I246T	NM_003467	NP_003458	P61073	CXCR4_HUMAN	chemokine (C-X-C motif) receptor 4 isoform b	261	Helical; Name=6.				activation of MAPK activity|apoptosis|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|entry into host cell|inflammatory response|initiation of viral infection|regulation of chemotaxis|response to hypoxia|response to virus	cell leading edge|cell surface|cytoplasmic membrane-bounded vesicle|integral to membrane|plasma membrane	actin binding|C-X-C chemokine receptor activity|coreceptor activity|myosin light chain binding|ubiquitin binding|ubiquitin protein ligase binding			upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.155)	Framycetin(DB00452)													---	---	---	---
THSD7B	80731	broad.mit.edu	37	2	137928399	137928399	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137928399G>T	uc002tva.1	+	6	1521	c.1521G>T	c.(1519-1521)GAG>GAT	p.E507D	THSD7B_uc010zbj.1_Intron|THSD7B_uc002tvb.2_Missense_Mutation_p.E397D	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	138169211	138169211	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138169211T>C	uc002tva.1	+	13	2635	c.2635T>C	c.(2635-2637)TCT>CCT	p.S879P	THSD7B_uc010zbj.1_Intron|THSD7B_uc002tvb.2_Missense_Mutation_p.S769P	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)														---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	141597656	141597656	+	Splice_Site	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141597656T>G	uc002tvj.1	-	31	6087	c.5115_splice	c.e31-1	p.G1705_splice		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)			---	---	---	---
LYPD6	130574	broad.mit.edu	37	2	150305638	150305638	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150305638C>T	uc002twy.2	+	3	389	c.194C>T	c.(193-195)GCT>GTT	p.A65V	LYPD6_uc010fnt.2_RNA|LYPD6_uc002twz.2_RNA|LYPD6_uc002txa.2_Missense_Mutation_p.A65V	NM_194317	NP_919298	Q86Y78	LYPD6_HUMAN	LY6/PLAUR domain containing 6 precursor	65	UPAR/Ly6.					extracellular region					0				BRCA - Breast invasive adenocarcinoma(221;0.0667)														---	---	---	---
LYPD6	130574	broad.mit.edu	37	2	150325226	150325226	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150325226C>T	uc002twy.2	+	4	480	c.285C>T	c.(283-285)CGC>CGT	p.R95R	LYPD6_uc010fnt.2_RNA|LYPD6_uc002twz.2_RNA|LYPD6_uc002txa.2_Silent_p.R95R	NM_194317	NP_919298	Q86Y78	LYPD6_HUMAN	LY6/PLAUR domain containing 6 precursor	95	UPAR/Ly6.					extracellular region					0				BRCA - Breast invasive adenocarcinoma(221;0.0667)														---	---	---	---
NEB	4703	broad.mit.edu	37	2	152473908	152473908	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152473908T>C	uc010fnx.2	-	71	10613	c.10422A>G	c.(10420-10422)TTA>TTG	p.L3474L		NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	3474	Nebulin 95.				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)														---	---	---	---
NR4A2	4929	broad.mit.edu	37	2	157186152	157186152	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157186152G>T	uc002tyz.3	-	3	969	c.547C>A	c.(547-549)CCT>ACT	p.P183T	NR4A2_uc002tyx.3_Missense_Mutation_p.P120T|NR4A2_uc010zcf.1_Missense_Mutation_p.P183T|NR4A2_uc010zcg.1_5'Flank	NM_006186	NP_006177	P43354	NR4A2_HUMAN	nuclear receptor subfamily 4, group A, member 2	183	Pro-rich.				cellular response to extracellular stimulus|dopaminergic neuron differentiation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to protein stimulus	nucleoplasm	sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(3)	3																		---	---	---	---
TANC1	85461	broad.mit.edu	37	2	160042340	160042340	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160042340A>G	uc002uag.2	+	15	2823	c.2549A>G	c.(2548-2550)CAG>CGG	p.Q850R	TANC1_uc010zcm.1_Missense_Mutation_p.Q842R|TANC1_uc010fom.1_Missense_Mutation_p.Q656R	NM_033394	NP_203752	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and	850						cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3																OREG0015033	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TANC1	85461	broad.mit.edu	37	2	160087092	160087092	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160087092C>A	uc002uag.2	+	27	5429	c.5155C>A	c.(5155-5157)CGC>AGC	p.R1719S	TANC1_uc010zcm.1_3'UTR|TANC1_uc010fon.2_Missense_Mutation_p.R563S	NM_033394	NP_203752	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and	1719						cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
COBLL1	22837	broad.mit.edu	37	2	165550975	165550975	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165550975G>A	uc010zcw.1	-	15	3366	c.3242C>T	c.(3241-3243)GCC>GTC	p.A1081V	COBLL1_uc002ucp.2_Missense_Mutation_p.A1014V|COBLL1_uc002ucq.2_Missense_Mutation_p.A976V|COBLL1_uc010zcx.1_Missense_Mutation_p.A1022V|COBLL1_uc002ucn.2_Missense_Mutation_p.A442V|COBLL1_uc002uco.2_Missense_Mutation_p.A745V	NM_014900	NP_055715	Q53SF7	COBL1_HUMAN	COBL-like 1	1052										ovary(2)|pancreas(1)	3																		---	---	---	---
COBLL1	22837	broad.mit.edu	37	2	165552145	165552145	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165552145A>G	uc010zcw.1	-	15	2196	c.2072T>C	c.(2071-2073)GTA>GCA	p.V691A	COBLL1_uc002ucp.2_Missense_Mutation_p.V624A|COBLL1_uc002ucq.2_Missense_Mutation_p.V586A|COBLL1_uc010zcx.1_Missense_Mutation_p.V632A|COBLL1_uc002ucn.2_Missense_Mutation_p.V52A|COBLL1_uc002uco.2_Missense_Mutation_p.V355A	NM_014900	NP_055715	Q53SF7	COBL1_HUMAN	COBL-like 1	662										ovary(2)|pancreas(1)	3																		---	---	---	---
CSRNP3	80034	broad.mit.edu	37	2	166536088	166536088	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166536088A>G	uc002udf.2	+	7	1959	c.1583A>G	c.(1582-1584)CAA>CGA	p.Q528R	CSRNP3_uc002udg.2_Missense_Mutation_p.Q528R	NM_024969	NP_079245	Q8WYN3	CSRN3_HUMAN	cysteine-serine-rich nuclear protein 3	528					apoptosis|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|large_intestine(1)|skin(1)	5																		---	---	---	---
XIRP2	129446	broad.mit.edu	37	2	168104598	168104598	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168104598C>T	uc002udx.2	+	8	6714	c.6696C>T	c.(6694-6696)CAC>CAT	p.H2232H	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Silent_p.H2057H|XIRP2_uc010fpq.2_Silent_p.H2010H|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_Intron	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	2057					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14																		---	---	---	---
XIRP2	129446	broad.mit.edu	37	2	168105123	168105123	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168105123T>C	uc002udx.2	+	8	7239	c.7221T>C	c.(7219-7221)TCT>TCC	p.S2407S	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Silent_p.S2232S|XIRP2_uc010fpq.2_Silent_p.S2185S|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_Intron	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	2232					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14																		---	---	---	---
OLA1	29789	broad.mit.edu	37	2	174943799	174943799	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174943799T>G	uc002uih.2	-	10	1172	c.986A>C	c.(985-987)CAG>CCG	p.Q329P	OLA1_uc002uii.2_Missense_Mutation_p.Q171P|OLA1_uc010fqq.2_Missense_Mutation_p.Q308P|OLA1_uc002uij.2_Missense_Mutation_p.Q171P|OLA1_uc002uik.2_Missense_Mutation_p.Q299P|OLA1_uc010fqr.2_Intron	NM_013341	NP_037473	Q9NTK5	OLA1_HUMAN	Obg-like ATPase 1 isoform 1	329					ATP catabolic process	cytoplasm	ATP binding|GTP binding|hydrolase activity|protein binding			ovary(1)|breast(1)	2																		---	---	---	---
TTN	7273	broad.mit.edu	37	2	179407678	179407678	+	Splice_Site	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179407678T>C	uc010zfg.1	-	297	89425	c.89201_splice	c.e297-1	p.V29734_splice	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Splice_Site_p.V23429_splice|TTN_uc010zfi.1_Splice_Site_p.V23362_splice|TTN_uc010zfj.1_Splice_Site_p.V23237_splice	NM_133378	NP_596869			titin isoform N2-A								ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179410683	179410683	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179410683G>A	uc010zfg.1	-	292	87800	c.87576C>T	c.(87574-87576)GGC>GGT	p.G29192G	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Silent_p.G22887G|TTN_uc010zfi.1_Silent_p.G22820G|TTN_uc010zfj.1_Silent_p.G22695G	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	30119							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	179430673	179430673	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179430673G>A	uc010zfg.1	-	275	72706	c.72482C>T	c.(72481-72483)GCG>GTG	p.A24161V	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.A17856V|TTN_uc010zfi.1_Missense_Mutation_p.A17789V|TTN_uc010zfj.1_Missense_Mutation_p.A17664V	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	25088							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	179435772	179435772	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179435772T>G	uc010zfg.1	-	275	67607	c.67383A>C	c.(67381-67383)AAA>AAC	p.K22461N	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.K16156N|TTN_uc010zfi.1_Missense_Mutation_p.K16089N|TTN_uc010zfj.1_Missense_Mutation_p.K15964N	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	23388							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	179470002	179470002	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179470002G>A	uc010zfg.1	-	229	46422	c.46198C>T	c.(46198-46200)CGT>TGT	p.R15400C	uc002umo.2_RNA|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.R9095C|TTN_uc010zfi.1_Missense_Mutation_p.R9028C|TTN_uc010zfj.1_Missense_Mutation_p.R8903C	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	16327							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	179475801	179475801	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179475801G>T	uc010zfg.1	-	219	43575	c.43351C>A	c.(43351-43353)CGT>AGT	p.R14451S	uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.R8146S|TTN_uc010zfi.1_Missense_Mutation_p.R8079S|TTN_uc010zfj.1_Missense_Mutation_p.R7954S	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	15378							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	179643641	179643641	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179643641G>A	uc010zfg.1	-	24	4392	c.4168C>T	c.(4168-4170)CCG>TCG	p.P1390S	TTN_uc010zfh.1_Missense_Mutation_p.P1344S|TTN_uc010zfi.1_Missense_Mutation_p.P1344S|TTN_uc010zfj.1_Missense_Mutation_p.P1344S|TTN_uc002unb.2_Missense_Mutation_p.P1390S|uc002unc.1_Intron	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	1390							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
CCDC141	285025	broad.mit.edu	37	2	179733869	179733869	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179733869A>G	uc002unf.1	-	5	701	c.644T>C	c.(643-645)GTC>GCC	p.V215A		NM_173648	NP_775919	Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	215							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)															---	---	---	---
ITGA4	3676	broad.mit.edu	37	2	182346400	182346400	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182346400A>G	uc002unu.2	+	7	1593	c.830A>G	c.(829-831)CAG>CGG	p.Q277R	ITGA4_uc010zfl.1_Missense_Mutation_p.Q277R	NM_000885	NP_000876	P13612	ITA4_HUMAN	integrin alpha 4 precursor	277	FG-GAP 4.|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)													---	---	---	---
COL3A1	1281	broad.mit.edu	37	2	189850511	189850511	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189850511C>T	uc002uqj.1	+							NM_000090	NP_000081			collagen type III alpha 1 preproprotein						axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway	collagen type III|extracellular space	extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding			central_nervous_system(7)|ovary(4)|large_intestine(2)	13			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)|Palifermin(DB00039)													---	---	---	---
MSTN	2660	broad.mit.edu	37	2	190927170	190927170	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190927170T>C	uc002urp.2	-	1	286	c.153A>G	c.(151-153)TCA>TCG	p.S51S		NM_005259	NP_005250	O14793	GDF8_HUMAN	myostatin precursor	51					muscle organ development|positive regulation of transcription, DNA-dependent	extracellular space	cytokine activity|growth factor activity			lung(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.000742)|Epithelial(96;0.0121)|all cancers(119;0.0395)															---	---	---	---
HIBCH	26275	broad.mit.edu	37	2	191175470	191175470	+	Intron	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191175470A>G	uc002uru.2	-						HIBCH_uc002urv.2_Intron	NM_014362	NP_055177			3-hydroxyisobutyryl-Coenzyme A hydrolase isoform						branched chain family amino acid catabolic process	mitochondrial matrix	3-hydroxyisobutyryl-CoA hydrolase activity|protein binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.000586)|Epithelial(96;0.0286)|all cancers(119;0.0814)															---	---	---	---
MFSD6	54842	broad.mit.edu	37	2	191364859	191364859	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191364859A>G	uc002urz.2	+	8	2615	c.2291A>G	c.(2290-2292)CAG>CGG	p.Q764R	MFSD6_uc010zge.1_Missense_Mutation_p.Q226R	NM_017694	NP_060164	Q6ZSS7	MFSD6_HUMAN	major facilitator superfamily domain containing	764					transmembrane transport	integral to membrane				ovary(2)	2																		---	---	---	---
DNAH7	56171	broad.mit.edu	37	2	196642721	196642721	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196642721C>T	uc002utj.3	-						DNAH7_uc002uti.3_Intron	NM_018897	NP_061720			dynein, axonemal, heavy chain 7						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12																		---	---	---	---
HECW2	57520	broad.mit.edu	37	2	197157407	197157407	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197157407G>A	uc002utm.1	-	14	3065	c.2882C>T	c.(2881-2883)ACC>ATC	p.T961I	HECW2_uc002utl.1_Missense_Mutation_p.T605I	NM_020760	NP_065811	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin	961	Interaction with TP73.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm	ubiquitin-protein ligase activity			skin(5)|ovary(5)|lung(4)|pancreas(2)|central_nervous_system(1)|kidney(1)	18																		---	---	---	---
ANKRD44	91526	broad.mit.edu	37	2	197878243	197878243	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197878243T>C	uc002uua.1	-	18	1918	c.1841A>G	c.(1840-1842)CAT>CGT	p.H614R	ANKRD44_uc002utz.3_Missense_Mutation_p.H346R	NM_153697	NP_710181	Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	639	ANK 19.						protein binding			ovary(4)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.246)															---	---	---	---
CD28	940	broad.mit.edu	37	2	204591381	204591381	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204591381G>A	uc002vah.3	+	2	300	c.78G>A	c.(76-78)TCG>TCA	p.S26S	CD28_uc002vag.1_RNA|CD28_uc010zio.1_RNA|CD28_uc010ftx.2_Intron|CD28_uc002vaj.3_RNA	NM_006139	NP_006130	P10747	CD28_HUMAN	CD28 antigen precursor	26	Extracellular (Potential).				cell surface receptor linked signaling pathway|cytokine biosynthetic process|humoral immune response|positive regulation of anti-apoptosis|positive regulation of interleukin-2 biosynthetic process|positive regulation of mitosis|positive regulation of translation|positive regulation of viral genome replication|regulation of defense response to virus by virus|regulatory T cell differentiation|T cell costimulation|viral reproduction	cytosol|external side of plasma membrane|integral to plasma membrane	coreceptor activity|protease binding|SH3/SH2 adaptor activity				0																		---	---	---	---
NDUFS1	4719	broad.mit.edu	37	2	207011641	207011641	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207011641C>T	uc002vbe.2	-	8	850	c.723G>A	c.(721-723)CGG>CGA	p.R241R	NDUFS1_uc010ziq.1_Silent_p.R255R|NDUFS1_uc010zir.1_Silent_p.R205R|NDUFS1_uc010zis.1_Silent_p.R184R|NDUFS1_uc010zit.1_Silent_p.R130R|NDUFS1_uc010ziu.1_Silent_p.R125R	NM_005006	NP_004997	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1,	241			R -> W (in MT-C1D).		apoptosis|ATP metabolic process|mitochondrial electron transport, NADH to ubiquinone|reactive oxygen species metabolic process|regulation of mitochondrial membrane potential|transport	mitochondrial intermembrane space|mitochondrial respiratory chain complex I	2 iron, 2 sulfur cluster binding|4 iron, 4 sulfur cluster binding|electron carrier activity|metal ion binding|NADH dehydrogenase (ubiquinone) activity|protein binding			ovary(1)	1					NADH(DB00157)													---	---	---	---
ATIC	471	broad.mit.edu	37	2	216182927	216182927	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216182927T>C	uc002vex.3	+	3	368	c.194T>C	c.(193-195)GTG>GCG	p.V65A	ATIC_uc010zjo.1_Missense_Mutation_p.V6A|ATIC_uc002vey.3_Missense_Mutation_p.V64A	NM_004044	NP_004035	P31939	PUR9_HUMAN	5-aminoimidazole-4-carboxamide ribonucleotide	65	IMP.				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								---	---	---	---
SMARCAL1	50485	broad.mit.edu	37	2	217280223	217280223	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217280223C>T	uc002vgc.3	+	3	1126	c.796C>T	c.(796-798)CCC>TCC	p.P266S	SMARCAL1_uc010fvf.2_RNA|SMARCAL1_uc002vgd.3_Missense_Mutation_p.P266S|SMARCAL1_uc010fvg.2_Missense_Mutation_p.P266S	NM_014140	NP_054859	Q9NZC9	SMAL1_HUMAN	SWI/SNF-related matrix-associated	266	HARP 1.				chromatin modification|DNA metabolic process|regulation of transcription from RNA polymerase II promoter	nucleus	ATP binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity			ovary(3)|breast(3)|skin(1)	7		Renal(323;0.0458)		Epithelial(149;9.48e-06)|all cancers(144;0.000621)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0111)										Schimke_Immuno-Osseous_Dysplasia				---	---	---	---
DES	1674	broad.mit.edu	37	2	220286147	220286147	+	Missense_Mutation	SNP	T	C	C	rs59308628		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220286147T>C	uc002vll.2	+	6	1195	c.1109T>C	c.(1108-1110)CTG>CCG	p.L370P		NM_001927	NP_001918	P17661	DESM_HUMAN	desmin	370	Rod.|Coil 2B.				cytoskeleton organization|muscle filament sliding|regulation of heart contraction	cytosol|Z disc	protein binding|structural constituent of cytoskeleton			central_nervous_system(2)	2		Renal(207;0.0183)		Epithelial(149;5.25e-07)|all cancers(144;0.000103)|Lung(261;0.00533)|LUSC - Lung squamous cell carcinoma(224;0.008)														---	---	---	---
IRS1	3667	broad.mit.edu	37	2	227662300	227662300	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227662300C>T	uc002voh.3	-	1	1207	c.1155G>A	c.(1153-1155)TCG>TCA	p.S385S		NM_005544	NP_005535	P35568	IRS1_HUMAN	insulin receptor substrate 1	385	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)	---	---	---	---
NEU2	4759	broad.mit.edu	37	2	233899329	233899329	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233899329C>T	uc010zmn.1	+	2	705	c.705C>T	c.(703-705)AAC>AAT	p.N235N		NM_005383	NP_005374	Q9Y3R4	NEUR2_HUMAN	neuraminidase 2	235							exo-alpha-sialidase activity				0		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0271)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0839)		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0488)														---	---	---	---
AGAP1	116987	broad.mit.edu	37	2	236877255	236877255	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236877255G>A	uc002vvs.2	+	13	2228	c.1633G>A	c.(1633-1635)GGC>AGC	p.G545S	AGAP1_uc002vvt.2_Missense_Mutation_p.G492S	NM_001037131	NP_001032208	Q9UPQ3	AGAP1_HUMAN	centaurin, gamma 2 isoform 1	545	PH.				protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
CAPN10	11132	broad.mit.edu	37	2	241535788	241535788	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241535788C>T	uc002vzk.1	+	8	1515	c.1331C>T	c.(1330-1332)GCT>GTT	p.A444V	CAPN10_uc002vzl.1_Intron|CAPN10_uc002vzm.1_Intron|CAPN10_uc002vzn.1_Missense_Mutation_p.A316V|CAPN10_uc002vzo.1_RNA|CAPN10_uc010fzg.1_RNA|CAPN10_uc002vzp.1_RNA|CAPN10_uc002vzq.1_Intron	NM_023083	NP_075571	Q9HC96	CAN10_HUMAN	calpain 10 isoform a	444	Domain III 1.				actin cytoskeleton reorganization|cellular response to insulin stimulus|positive regulation of apoptosis|positive regulation of glucose import|positive regulation of insulin secretion|positive regulation of intracellular transport|proteolysis	cytosol|plasma membrane	calcium-dependent cysteine-type endopeptidase activity|cytoskeletal protein binding|SNARE binding			ovary(3)|large_intestine(2)|lung(1)	6		all_epithelial(40;1.72e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|all_neural(83;0.0459)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.13e-31)|all cancers(36;3.24e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.82e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;5.1e-06)|Lung(119;0.00168)|Colorectal(34;0.00495)|LUSC - Lung squamous cell carcinoma(224;0.00813)|COAD - Colon adenocarcinoma(134;0.032)														---	---	---	---
STK25	10494	broad.mit.edu	37	2	242438156	242438156	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242438156C>T	uc002wbm.2	-	7	1086	c.815G>A	c.(814-816)CGC>CAC	p.R272H	STK25_uc002wbk.2_Missense_Mutation_p.R91H|STK25_uc002wbl.2_3'UTR|STK25_uc002wbn.2_Missense_Mutation_p.R272H|STK25_uc002wbo.2_Missense_Mutation_p.R195H|STK25_uc010zos.1_Missense_Mutation_p.R178H|STK25_uc010zot.1_Missense_Mutation_p.R198H|STK25_uc002wbp.2_Missense_Mutation_p.R272H|STK25_uc010fzo.2_Missense_Mutation_p.R195H|STK25_uc010zou.1_Missense_Mutation_p.R178H|STK25_uc010zov.1_Missense_Mutation_p.R178H	NM_006374	NP_006365	O00506	STK25_HUMAN	serine/threonine kinase 25	272					response to oxidative stress|signal transduction	Golgi apparatus	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity				0		all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2)		Epithelial(32;8.24e-34)|all cancers(36;3.46e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.6e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.1e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0839)														---	---	---	---
CNTN6	27255	broad.mit.edu	37	3	1415736	1415736	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1415736T>G	uc003boz.2	+	16	2341	c.2074T>G	c.(2074-2076)TTG>GTG	p.L692V	CNTN6_uc011asj.1_Missense_Mutation_p.L620V|CNTN6_uc003bpa.2_Missense_Mutation_p.L692V	NM_014461	NP_055276	Q9UQ52	CNTN6_HUMAN	contactin 6 precursor	692	Fibronectin type-III 1.				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)														---	---	---	---
SETD5	55209	broad.mit.edu	37	3	9512469	9512469	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9512469A>G	uc003brt.2	+	19	3486	c.3051A>G	c.(3049-3051)GGA>GGG	p.G1017G	SETD5_uc003bru.2_Silent_p.G919G|SETD5_uc003brv.2_Silent_p.G906G|SETD5_uc010hck.2_Silent_p.G499G|SETD5_uc003brx.2_Silent_p.G686G	NM_001080517	NP_001073986	Q9C0A6	SETD5_HUMAN	SET domain containing 5	1017										ovary(2)	2	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)														---	---	---	---
MTMR14	64419	broad.mit.edu	37	3	9731699	9731699	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9731699A>C	uc003brz.2	+	17	1609	c.1485A>C	c.(1483-1485)CAA>CAC	p.Q495H	MTMR14_uc003bsa.2_Missense_Mutation_p.Q495H|MTMR14_uc003bsb.2_Intron|MTMR14_uc011ath.1_Intron|MTMR14_uc010hcl.2_Intron|MTMR14_uc003bsc.2_Intron	NM_001077525	NP_001070993	Q8NCE2	MTMRE_HUMAN	jumpy isoform 2	495						perinuclear region of cytoplasm|ruffle	phosphatidylinositol-3-phosphatase activity|protein tyrosine phosphatase activity			skin(1)	1	Medulloblastoma(99;0.227)																	---	---	---	---
SLC6A11	6538	broad.mit.edu	37	3	10858168	10858168	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10858168T>C	uc003bvz.2	+	1	252	c.218T>C	c.(217-219)GTG>GCG	p.V73A	SLC6A11_uc003bvy.1_Missense_Mutation_p.V73A	NM_014229	NP_055044	P48066	S6A11_HUMAN	solute carrier family 6 (neurotransmitter	73	Helical; Name=1; (Potential).				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)														---	---	---	---
IQSEC1	9922	broad.mit.edu	37	3	12953174	12953174	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12953174A>G	uc003bxt.2	-	10	2422	c.2413T>C	c.(2413-2415)TCC>CCC	p.S805P	IQSEC1_uc003bxu.3_Missense_Mutation_p.S683P|IQSEC1_uc011auw.1_Missense_Mutation_p.S791P	NM_014869	NP_055684	Q6DN90	IQEC1_HUMAN	IQ motif and Sec7 domain 1 isoform b	805	PH.				regulation of ARF protein signal transduction	cytoplasm|nucleus	ARF guanyl-nucleotide exchange factor activity			ovary(1)	1																		---	---	---	---
XPC	7508	broad.mit.edu	37	3	14207008	14207008	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14207008G>A	uc011ave.1	-	6	803	c.699C>T	c.(697-699)GGC>GGT	p.G233G	XPC_uc011avf.1_Silent_p.G40G|XPC_uc011avg.1_Silent_p.G196G	NM_004628	NP_004619	Q01831	XPC_HUMAN	xeroderma pigmentosum, complementation group C	233					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				---	---	---	---
NR2C2	7182	broad.mit.edu	37	3	15062266	15062266	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15062266A>G	uc003bzj.3	+	5	600	c.383A>G	c.(382-384)CAC>CGC	p.H128R	NR2C2_uc003bzi.2_Missense_Mutation_p.H147R	NM_003298	NP_003289	P49116	NR2C2_HUMAN	nuclear receptor subfamily 2, group C, member 2	128	Nuclear receptor.|NR C4-type.				cell differentiation|nervous system development|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|spermatogenesis	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription coactivator activity|zinc ion binding				0																		---	---	---	---
ANKRD28	23243	broad.mit.edu	37	3	15727634	15727634	+	Intron	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15727634A>G	uc003caj.1	-						ANKRD28_uc003cai.1_Intron|ANKRD28_uc011avz.1_Intron|ANKRD28_uc003cak.1_Intron|ANKRD28_uc011awa.1_Intron|ANKRD28_uc003cal.1_Intron|ANKRD28_uc003cam.2_Intron	NM_015199	NP_056014			ankyrin repeat domain 28							nucleoplasm	protein binding			breast(1)	1																		---	---	---	---
NR1D2	9975	broad.mit.edu	37	3	24003698	24003698	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24003698A>G	uc003ccs.2	+	5	1067	c.748A>G	c.(748-750)AAG>GAG	p.K250E	NR1D2_uc010hfd.2_RNA|NR1D2_uc011awk.1_Missense_Mutation_p.K175E	NM_005126	NP_005117	Q14995	NR1D2_HUMAN	nuclear receptor subfamily 1, group D, member 2	250					regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	sequence-specific DNA binding|steroid hormone receptor activity|zinc ion binding			urinary_tract(1)|kidney(1)|skin(1)	3																		---	---	---	---
TMPPE	643853	broad.mit.edu	37	3	33134910	33134910	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33134910C>T	uc003cfk.2	-	2	969	c.778G>A	c.(778-780)GCT>ACT	p.A260T	GLB1_uc003cfh.1_Intron|GLB1_uc003cfi.1_Intron|GLB1_uc003cfj.1_Intron|GLB1_uc011axk.1_Intron|TMPPE_uc011axl.1_Missense_Mutation_p.A123T	NM_001039770	NP_001034859	Q6ZT21	TMPPE_HUMAN	transmembrane protein with	260						integral to membrane	metal ion binding				0																		---	---	---	---
ITGA9	3680	broad.mit.edu	37	3	37783282	37783282	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37783282A>G	uc003chd.2	+	21	2349	c.2296A>G	c.(2296-2298)ATG>GTG	p.M766V		NM_002207	NP_002198	Q13797	ITA9_HUMAN	integrin, alpha 9 precursor	766	Extracellular (Potential).				axon guidance|cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			breast(3)|pancreas(1)|lung(1)|skin(1)	6				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)														---	---	---	---
SCN5A	6331	broad.mit.edu	37	3	38592887	38592887	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38592887T>C	uc003cio.2	-	28	5170	c.4976A>G	c.(4975-4977)AAC>AGC	p.N1659S	SCN5A_uc003cin.2_Missense_Mutation_p.N1658S|SCN5A_uc003cil.3_Missense_Mutation_p.N1659S|SCN5A_uc010hhi.2_Missense_Mutation_p.N1641S|SCN5A_uc010hhk.2_Missense_Mutation_p.N1626S|SCN5A_uc011ayr.1_Missense_Mutation_p.N1605S	NM_198056	NP_932173	Q14524	SCN5A_HUMAN	voltage-gated sodium channel type V alpha	1659					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)													---	---	---	---
KIF15	56992	broad.mit.edu	37	3	44846542	44846542	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44846542G>A	uc003cnx.3	+	15	1860	c.1711G>A	c.(1711-1713)GCT>ACT	p.A571T	KIF15_uc010hiq.2_Missense_Mutation_p.A474T|KIF15_uc003cny.1_Missense_Mutation_p.A206T	NM_020242	NP_064627	Q9NS87	KIF15_HUMAN	kinesin family member 15	571	Potential.				blood coagulation|cell proliferation|microtubule-based movement|mitosis	centrosome|cytosol|microtubule|plus-end kinesin complex|spindle	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)														---	---	---	---
CCR9	10803	broad.mit.edu	37	3	45942329	45942329	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45942329T>C	uc003coz.1	+	3	206	c.49T>C	c.(49-51)TAT>CAT	p.Y17H	LZTFL1_uc003coy.1_Intron|LZTFL1_uc011bak.1_Intron|CCR9_uc010hiv.1_Missense_Mutation_p.Y5H|CCR9_uc003cpa.1_Missense_Mutation_p.Y5H	NM_031200	NP_112477	P51686	CCR9_HUMAN	chemokine (C-C motif) receptor 9 isoform A	17	Extracellular (Potential).				cellular defense response|chemotaxis|elevation of cytosolic calcium ion concentration|immune response	integral to plasma membrane				ovary(2)|breast(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.00118)|KIRC - Kidney renal clear cell carcinoma(197;0.0182)|Kidney(197;0.0214)														---	---	---	---
NBEAL2	23218	broad.mit.edu	37	3	47049831	47049831	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47049831C>A	uc003cqp.2	+	51	7957	c.7778C>A	c.(7777-7779)CCT>CAT	p.P2593H	NBEAL2_uc010hjm.1_Missense_Mutation_p.P1970H|NBEAL2_uc010hjn.1_Missense_Mutation_p.P959H|NBEAL2_uc010hjo.1_Missense_Mutation_p.P153H	NM_015175	NP_055990	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	2593							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)														---	---	---	---
ZNF589	51385	broad.mit.edu	37	3	48310095	48310095	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48310095T>A	uc003csl.3	+	4	980	c.914T>A	c.(913-915)GTG>GAG	p.V305E	ZNF589_uc010hjt.1_Missense_Mutation_p.V302E|ZNF589_uc003csn.2_RNA|ZNF589_uc011bbg.1_Intron|ZNF589_uc003csm.2_Intron	NM_016089	NP_057173	Q86UQ0	ZN589_HUMAN	zinc finger protein 589	305	C2H2-type 3.				regulation of transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000649)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)														---	---	---	---
COL7A1	1294	broad.mit.edu	37	3	48605200	48605200	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48605200C>T	uc003ctz.2	-							NM_000094	NP_000085			alpha 1 type VII collagen precursor						cell adhesion|epidermis development	basement membrane|collagen type VII	protein binding|serine-type endopeptidase inhibitor activity			ovary(4)|breast(3)|skin(3)|central_nervous_system(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)														---	---	---	---
COL7A1	1294	broad.mit.edu	37	3	48630681	48630681	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48630681T>C	uc003ctz.2	-	5	537	c.536A>G	c.(535-537)GAC>GGC	p.D179G		NM_000094	NP_000085	Q02388	CO7A1_HUMAN	alpha 1 type VII collagen precursor	179	Nonhelical region (NC1).|VWFA 1.				cell adhesion|epidermis development	basement membrane|collagen type VII	protein binding|serine-type endopeptidase inhibitor activity			ovary(4)|breast(3)|skin(3)|central_nervous_system(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)														---	---	---	---
CELSR3	1951	broad.mit.edu	37	3	48670430	48670430	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48670430C>T	uc003cuf.1	-	39	10592	c.10592G>A	c.(10591-10593)GGC>GAC	p.G3531D	SLC26A6_uc003cug.2_Missense_Mutation_p.G116D|SLC26A6_uc003cuh.2_Missense_Mutation_p.G137D|SLC26A6_uc010hke.2_5'UTR|SLC26A6_uc003cuk.2_Missense_Mutation_p.G137D|SLC26A6_uc003cui.2_Missense_Mutation_p.G137D|SLC26A6_uc003cuj.2_Missense_Mutation_p.G137D|SLC26A6_uc011bbp.1_Missense_Mutation_p.G137D	NM_001407	NP_001398	Q9NYQ7	CELR3_HUMAN	cadherin EGF LAG seven-pass G-type receptor 3	Error:Variant_position_missing_in_Q9NYQ7_after_alignment					homophilic cell adhesion|multicellular organismal development|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(5)|upper_aerodigestive_tract(2)|central_nervous_system(2)|skin(2)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)														---	---	---	---
MST1R	4486	broad.mit.edu	37	3	49929220	49929220	+	Missense_Mutation	SNP	C	T	T	rs147999292		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49929220C>T	uc003cxy.3	-	15	3587	c.3323G>A	c.(3322-3324)CGA>CAA	p.R1108Q	MST1R_uc011bdc.1_5'UTR	NM_002447	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor precursor	1108	Cytoplasmic (Potential).|Protein kinase.				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)														---	---	---	---
MON1A	84315	broad.mit.edu	37	3	49949050	49949050	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49949050A>G	uc003cxz.2	-	3	939	c.813T>C	c.(811-813)TCT>TCC	p.S271S	MON1A_uc003cya.2_Intron|MON1A_uc003cyb.2_Intron	NM_032355	NP_115731	Q86VX9	MON1A_HUMAN	MON1 homolog A isoform a	174							protein binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)														---	---	---	---
NPRL2	10641	broad.mit.edu	37	3	50385604	50385604	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50385604G>A	uc003daj.1	-	9	1286	c.883C>T	c.(883-885)CGA>TGA	p.R295*	ZMYND10_uc003dag.1_5'Flank|ZMYND10_uc010hll.1_5'Flank|ZMYND10_uc003dah.1_5'Flank|ZMYND10_uc010hlm.1_5'Flank|NPRL2_uc003dai.1_Nonsense_Mutation_p.R175*|CYB561D2_uc003dak.2_5'Flank|CYB561D2_uc003dal.2_5'Flank|CYB561D2_uc003dam.2_5'Flank	NM_006545	NP_006536	Q8WTW4	NPRL2_HUMAN	tumor suppressor candidate 4	295					negative regulation of kinase activity		protein binding|protein kinase activity			lung(1)	1																		---	---	---	---
ALAS1	211	broad.mit.edu	37	3	52236584	52236584	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52236584T>C	uc003dcy.1	+	4	598	c.261T>C	c.(259-261)GAT>GAC	p.D87D	ALAS1_uc003dcx.1_Silent_p.D87D|ALAS1_uc003dcz.1_Silent_p.D87D|ALAS1_uc011bec.1_Silent_p.D104D	NM_000688	NP_000679	P13196	HEM1_HUMAN	5-aminolevulinate synthase 1 precursor	87					heme biosynthetic process	mitochondrial matrix	5-aminolevulinate synthase activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups			ovary(2)|upper_aerodigestive_tract(1)	3				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.000583)|KIRC - Kidney renal clear cell carcinoma(197;0.000751)	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)													---	---	---	---
DNAH1	25981	broad.mit.edu	37	3	52394321	52394321	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52394321C>T	uc011bef.1	+							NM_015512	NP_056327			dynein, axonemal, heavy chain 1						ciliary or flagellar motility|microtubule-based movement|response to mechanical stimulus	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			large_intestine(3)	3				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)														---	---	---	---
PBRM1	55193	broad.mit.edu	37	3	52663053	52663053	+	Splice_Site	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52663053T>C	uc003des.2	-	12	1314	c.1302_splice	c.e12-1	p.R434_splice	PBRM1_uc003dex.2_Splice_Site|PBRM1_uc003deq.2_Splice_Site_p.R434_splice|PBRM1_uc003der.2_Splice_Site_p.R402_splice|PBRM1_uc003det.2_Splice_Site_p.R434_splice|PBRM1_uc003deu.2_Splice_Site_p.R434_splice|PBRM1_uc003dev.2_Splice_Site|PBRM1_uc003dew.2_Splice_Site_p.R434_splice|PBRM1_uc010hmk.1_Splice_Site_p.R434_splice|PBRM1_uc003dey.2_Splice_Site_p.R434_splice|PBRM1_uc003dez.1_Splice_Site_p.R434_splice|PBRM1_uc003dfb.1_Splice_Site_p.R332_splice	NM_181042	NP_060635			polybromo 1 isoform 4						chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)				Mis|N|F|S|D|O		clear cell renal carcinoma|breast								---	---	---	---
IL17RD	54756	broad.mit.edu	37	3	57131817	57131817	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57131817G>A	uc003dil.2	-	12	2003	c.1914C>T	c.(1912-1914)GAC>GAT	p.D638D	IL17RD_uc003dik.2_Silent_p.D614D|IL17RD_uc010hna.2_Silent_p.D494D|IL17RD_uc011bex.1_Silent_p.D494D	NM_017563	NP_060033	Q8NFM7	I17RD_HUMAN	interleukin 17 receptor D precursor	638	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)														---	---	---	---
ASB14	142686	broad.mit.edu	37	3	57310727	57310727	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57310727G>A	uc003diq.2	-	10	1711	c.1123C>T	c.(1123-1125)CGC>TGC	p.R375C	ASB14_uc003dip.1_Missense_Mutation_p.R254C	NM_001142733	NP_001136205	A6NK59	ASB14_HUMAN	ankyrin repeat and SOCS box-containing 14	539	SOCS box.				intracellular signal transduction						0				KIRC - Kidney renal clear cell carcinoma(284;0.011)|Kidney(284;0.0127)														---	---	---	---
C3orf67	200844	broad.mit.edu	37	3	58855205	58855205	+	Silent	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58855205G>T	uc003dkt.1	-	9	898	c.489C>A	c.(487-489)TCC>TCA	p.S163S	C3orf67_uc003dks.1_5'UTR|uc003dku.1_Intron|C3orf67_uc003dkv.1_5'UTR|C3orf67_uc003dkw.2_Silent_p.S71S	NM_198463	NP_940865	Q6ZVT6	CC067_HUMAN	hypothetical protein LOC200844	163											0		all_cancers(2;0.000156)|all_epithelial(2;0.000493)|Breast(2;0.00446)|all_lung(2;0.074)|Lung NSC(2;0.248)		BRCA - Breast invasive adenocarcinoma(55;5.93e-06)|Kidney(10;0.00155)|KIRC - Kidney renal clear cell carcinoma(10;0.00172)|OV - Ovarian serous cystadenocarcinoma(275;0.23)														---	---	---	---
CADPS	8618	broad.mit.edu	37	3	62478083	62478083	+	Silent	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62478083C>A	uc003dll.2	-	20	3126	c.2766G>T	c.(2764-2766)GCG>GCT	p.A922A	CADPS_uc003dlk.1_Silent_p.A419A|CADPS_uc003dlm.2_Silent_p.A932A|CADPS_uc003dln.2_Silent_p.A892A	NM_003716	NP_003707	Q9ULU8	CAPS1_HUMAN	Ca2+-dependent secretion activator isoform 1	922	Interaction with DRD2.				exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|cytosol|synapse	lipid binding|metal ion binding			central_nervous_system(2)|ovary(1)	3		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)														---	---	---	---
CADPS	8618	broad.mit.edu	37	3	62636607	62636607	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62636607C>T	uc003dll.2	-	5	1478	c.1118G>A	c.(1117-1119)AGC>AAC	p.S373N	CADPS_uc003dlm.2_Missense_Mutation_p.S373N|CADPS_uc003dln.2_Missense_Mutation_p.S373N	NM_003716	NP_003707	Q9ULU8	CAPS1_HUMAN	Ca2+-dependent secretion activator isoform 1	373					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)														---	---	---	---
ADAMTS9	56999	broad.mit.edu	37	3	64601636	64601636	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64601636T>G	uc003dmg.2	-	20	3056	c.3024A>C	c.(3022-3024)GAA>GAC	p.E1008D	ADAMTS9_uc011bfo.1_Missense_Mutation_p.E980D|ADAMTS9_uc003dmh.1_Missense_Mutation_p.E837D|ADAMTS9_uc003dmk.1_Missense_Mutation_p.E1008D|ADAMTS9_uc011bfp.1_5'UTR	NM_182920	NP_891550	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1008	TSP type-1 4.				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)														---	---	---	---
KBTBD8	84541	broad.mit.edu	37	3	67054184	67054184	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67054184T>C	uc003dmy.2	+	3	846	c.793T>C	c.(793-795)TGT>CGT	p.C265R	KBTBD8_uc011bfv.1_Intron	NM_032505	NP_115894	Q8NFY9	KBTB8_HUMAN	T-cell activation kelch repeat protein	265										ovary(2)|large_intestine(1)|breast(1)	4		Lung NSC(201;0.0765)		BRCA - Breast invasive adenocarcinoma(55;6.02e-06)|KIRC - Kidney renal clear cell carcinoma(39;0.105)|Kidney(39;0.125)														---	---	---	---
FOXP1	27086	broad.mit.edu	37	3	71026102	71026102	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71026102G>A	uc003dol.2	-	13	1843	c.1520C>T	c.(1519-1521)GCC>GTC	p.A507V	FOXP1_uc003dom.2_Missense_Mutation_p.A431V|FOXP1_uc003don.2_RNA|FOXP1_uc003doo.2_Missense_Mutation_p.A506V|FOXP1_uc003dop.2_Missense_Mutation_p.A507V|FOXP1_uc003doq.1_Intron|FOXP1_uc003doi.2_Missense_Mutation_p.A407V|FOXP1_uc003doj.2_Missense_Mutation_p.A407V|FOXP1_uc003dok.2_Missense_Mutation_p.A320V|FOXP1_uc003dor.1_Missense_Mutation_p.A284V	NM_032682	NP_116071	Q9H334	FOXP1_HUMAN	forkhead box P1 isoform 1	507	Fork-head.				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								---	---	---	---
DPPA4	55211	broad.mit.edu	37	3	109049430	109049430	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109049430G>A	uc003dxq.3	-	5	675	c.620C>T	c.(619-621)GCG>GTG	p.A207V	DPPA4_uc011bho.1_Intron|DPPA4_uc011bhp.1_Missense_Mutation_p.A207V	NM_018189	NP_060659	Q7L190	DPPA4_HUMAN	developmental pluripotency associated 4	207						nucleus	protein binding			upper_aerodigestive_tract(1)	1																		---	---	---	---
CCDC80	151887	broad.mit.edu	37	3	112358410	112358410	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112358410G>A	uc003dzf.2	-	2	561	c.343C>T	c.(343-345)CGT>TGT	p.R115C	CCDC80_uc011bhv.1_Missense_Mutation_p.R115C|CCDC80_uc003dzg.2_Missense_Mutation_p.R115C|CCDC80_uc003dzh.1_Missense_Mutation_p.R115C	NM_199512	NP_955806	Q76M96	CCD80_HUMAN	steroid-sensitive protein 1 precursor	115										ovary(2)	2																		---	---	---	---
CD200R1L	344807	broad.mit.edu	37	3	112545940	112545940	+	Silent	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112545940C>A	uc003dzi.1	-	4	805	c.579G>T	c.(577-579)ACG>ACT	p.T193T	CD200R1L_uc011bhw.1_Silent_p.T172T|CD200R1L_uc010hqf.1_Silent_p.T172T	NM_001008784	NP_001008784	Q6Q8B3	MO2R2_HUMAN	CD200 cell surface glycoprotein receptor 2	193	Extracellular (Potential).|Ig-like C2-type.					integral to membrane	receptor activity			ovary(1)	1																		---	---	---	---
CCDC52	152185	broad.mit.edu	37	3	113187166	113187166	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113187166A>G	uc003eag.3	-	10	1266	c.975T>C	c.(973-975)AAT>AAC	p.N325N	CCDC52_uc003eaf.3_RNA|CCDC52_uc003eah.1_Silent_p.N221N	NM_144718	NP_653319	Q8N0Z3	SPICE_HUMAN	coiled-coil domain containing 52	325	Potential.				cell division|mitosis	centriole|spindle	protein binding				0																		---	---	---	---
KIAA2018	205717	broad.mit.edu	37	3	113377745	113377745	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113377745A>G	uc003eam.2	-	7	3195	c.2784T>C	c.(2782-2784)AGT>AGC	p.S928S	KIAA2018_uc003eal.2_Silent_p.S872S	NM_001009899	NP_001009899	Q68DE3	K2018_HUMAN	hypothetical protein LOC205717	928					regulation of transcription, DNA-dependent	membrane|nucleus	calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			skin(2)|ovary(1)	3																		---	---	---	---
DRD3	1814	broad.mit.edu	37	3	113890577	113890577	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113890577T>C	uc003ebd.2	-	3	686	c.263A>G	c.(262-264)TAC>TGC	p.Y88C	DRD3_uc010hqn.1_Missense_Mutation_p.Y88C|DRD3_uc003ebb.1_Missense_Mutation_p.Y88C|DRD3_uc003ebc.1_Missense_Mutation_p.Y88C	NM_000796	NP_000787	P35462	DRD3_HUMAN	dopamine receptor D3 isoform a	88	Helical; Name=2.				activation of adenylate cyclase activity by dopamine receptor signaling pathway|arachidonic acid secretion|behavioral response to cocaine|cellular calcium ion homeostasis|circadian regulation of gene expression|G-protein coupled receptor internalization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|locomotory behavior|musculoskeletal movement, spinal reflex action|negative regulation of blood pressure|negative regulation of oligodendrocyte differentiation|negative regulation of protein kinase B signaling cascade|negative regulation of protein secretion|positive regulation of dopamine receptor signaling pathway|positive regulation of mitosis|prepulse inhibition|regulation of dopamine secretion|response to drug|response to histamine|response to morphine|social behavior|visual learning	integral to plasma membrane	dopamine D3 receptor activity|drug binding			ovary(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4					Apomorphine(DB00714)|Chlorprothixene(DB01239)|Cocaine(DB00907)|Methotrimeprazine(DB01403)|Olanzapine(DB00334)|Pramipexole(DB00413)|Ropinirole(DB00268)|Ziprasidone(DB00246)													---	---	---	---
TIGIT	201633	broad.mit.edu	37	3	114014510	114014510	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114014510G>A	uc003ebg.1	+	2	214	c.180G>A	c.(178-180)GAG>GAA	p.E60E		NM_173799	NP_776160	Q495A1	TIGIT_HUMAN	T cell immunoreceptor with Ig and ITIM domains	60	Extracellular (Potential).|Ig-like V-type.				negative regulation of interleukin-12 production|negative regulation of T cell activation|positive regulation of interleukin-10 production	cell surface|integral to membrane|plasma membrane	protein binding			central_nervous_system(1)	1																		---	---	---	---
ZBTB20	26137	broad.mit.edu	37	3	114070097	114070097	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114070097C>T	uc003ebi.2	-	4	1008	c.828G>A	c.(826-828)CTG>CTA	p.L276L	ZBTB20_uc003ebj.2_Silent_p.L203L|ZBTB20_uc010hqp.2_Silent_p.L203L|ZBTB20_uc003ebk.2_Silent_p.L203L|ZBTB20_uc003ebl.2_Silent_p.L203L|ZBTB20_uc003ebm.2_Silent_p.L203L|ZBTB20_uc003ebn.2_Silent_p.L203L|uc003ebo.1_5'Flank	NM_015642	NP_056457	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20 isoform	276					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)														---	---	---	---
HGD	3081	broad.mit.edu	37	3	120389319	120389319	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120389319G>A	uc003edw.2	-	4	607	c.237C>T	c.(235-237)GGC>GGT	p.G79G		NM_000187	NP_000178	Q93099	HGD_HUMAN	homogentisate 1,2-dioxygenase	79					L-phenylalanine catabolic process|tyrosine catabolic process	cytosol	homogentisate 1,2-dioxygenase activity|metal ion binding				0				GBM - Glioblastoma multiforme(114;0.158)														---	---	---	---
STXBP5L	9515	broad.mit.edu	37	3	120628445	120628445	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120628445G>A	uc003eec.3	+	2	160	c.20G>A	c.(19-21)CGA>CAA	p.R7Q	STXBP5L_uc011bji.1_Missense_Mutation_p.R7Q	NM_014980	NP_055795	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	7					exocytosis|protein transport	cytoplasm|integral to membrane|plasma membrane				ovary(7)|skin(2)	9				GBM - Glioblastoma multiforme(114;0.0694)														---	---	---	---
PARP9	83666	broad.mit.edu	37	3	122255825	122255825	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122255825C>A	uc010hri.2	-	9	2111	c.1966G>T	c.(1966-1968)GAT>TAT	p.D656Y	PARP9_uc003eff.3_Missense_Mutation_p.D621Y|PARP9_uc011bjs.1_Missense_Mutation_p.D621Y|PARP9_uc003efg.2_Missense_Mutation_p.D201Y|PARP9_uc003efi.2_Missense_Mutation_p.D621Y|PARP9_uc003efh.2_Missense_Mutation_p.D656Y|PARP9_uc003efj.2_Missense_Mutation_p.D621Y	NM_001146102	NP_001139574	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9	656	PARP catalytic.				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)														---	---	---	---
KALRN	8997	broad.mit.edu	37	3	124157813	124157813	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124157813C>T	uc003ehg.2	+	18	3248	c.3121C>T	c.(3121-3123)CCA>TCA	p.P1041S	KALRN_uc010hrv.1_Missense_Mutation_p.P1032S|KALRN_uc003ehf.1_Missense_Mutation_p.P1041S|KALRN_uc011bjy.1_Missense_Mutation_p.P1032S|KALRN_uc003ehh.1_Missense_Mutation_p.P387S	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1	1041					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																		---	---	---	---
ABTB1	80325	broad.mit.edu	37	3	127398914	127398914	+	Silent	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127398914G>T	uc003ejt.2	+	11	1204	c.1116G>T	c.(1114-1116)CTG>CTT	p.L372L	ABTB1_uc003ejr.2_Silent_p.L230L|ABTB1_uc003ejs.2_Silent_p.L347L|ABTB1_uc003eju.2_Silent_p.L230L|ABTB1_uc010hsm.2_Silent_p.L99L	NM_172027	NP_742024	Q969K4	ABTB1_HUMAN	ankyrin repeat and BTB (POZ) domain containing 1	372						cytoplasm|nucleolus|plasma membrane	translation elongation factor activity				0																		---	---	---	---
ACAD11	84129	broad.mit.edu	37	3	132358469	132358469	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132358469G>A	uc003eov.3	-	5	949	c.569C>T	c.(568-570)GCA>GTA	p.A190V	ACAD11_uc003eoy.2_Missense_Mutation_p.A190V	NM_032169	NP_115545	Q709F0	ACD11_HUMAN	putative acyl-CoA dehydrogenase	190						peroxisome	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|transferase activity, transferring phosphorus-containing groups			ovary(1)	1																		---	---	---	---
TF	7018	broad.mit.edu	37	3	133473387	133473387	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133473387G>A	uc003epu.1	+	9	2102	c.374G>A	c.(373-375)GGC>GAC	p.G125D	TF_uc011bls.1_Missense_Mutation_p.G125D|TF_uc011blt.1_5'UTR|TF_uc003epw.1_Intron|TF_uc003epv.1_Missense_Mutation_p.G125D	NM_001063	NP_001054	P02787	TRFE_HUMAN	transferrin precursor	125	Transferrin-like 1.				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)													---	---	---	---
ARMC8	25852	broad.mit.edu	37	3	137963957	137963957	+	Missense_Mutation	SNP	G	A	A	rs138240060		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137963957G>A	uc003esa.1	+	13	1391	c.1024G>A	c.(1024-1026)GAA>AAA	p.E342K	ARMC8_uc003erw.2_Missense_Mutation_p.E342K|ARMC8_uc003erx.2_Missense_Mutation_p.E342K|ARMC8_uc003ery.2_Missense_Mutation_p.E314K|ARMC8_uc003erz.2_Missense_Mutation_p.E314K|ARMC8_uc011bmf.1_Missense_Mutation_p.E325K|ARMC8_uc011bmg.1_Missense_Mutation_p.E289K|ARMC8_uc011bmh.1_Missense_Mutation_p.E283K|ARMC8_uc003esb.1_Missense_Mutation_p.E314K|ARMC8_uc003esc.1_Missense_Mutation_p.E114K	NM_015396	NP_056211	Q8IUR7	ARMC8_HUMAN	armadillo repeat containing 8 isoform 2	356							binding				0																		---	---	---	---
MRAS	22808	broad.mit.edu	37	3	138119364	138119364	+	Intron	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138119364T>G	uc003esh.3	+						MRAS_uc011bmi.1_Intron|MRAS_uc003esi.3_Intron|MRAS_uc011bmj.1_Intron	NM_012219	NP_036351			muscle RAS oncogene homolog precursor						actin cytoskeleton organization|muscle organ development|Ras protein signal transduction	intracellular|plasma membrane	GTP binding|GTP-dependent protein binding|GTPase activity			lung(2)|upper_aerodigestive_tract(1)|ovary(1)	4																		---	---	---	---
CEP70	80321	broad.mit.edu	37	3	138289294	138289294	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138289294G>A	uc003esl.2	-	6	529	c.331C>T	c.(331-333)CGA>TGA	p.R111*	CEP70_uc011bmk.1_Nonsense_Mutation_p.R91*|CEP70_uc011bml.1_Nonsense_Mutation_p.R93*|CEP70_uc011bmm.1_Intron|CEP70_uc003esm.2_Nonsense_Mutation_p.R111*|CEP70_uc003esn.2_Nonsense_Mutation_p.R111*	NM_024491	NP_077817	Q8NHQ1	CEP70_HUMAN	centrosomal protein 70 kDa	111	Potential.				G2/M transition of mitotic cell cycle	centrosome|cytosol	protein binding			skin(1)	1																		---	---	---	---
ZIC1	7545	broad.mit.edu	37	3	147130343	147130343	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147130343C>T	uc003ewe.2	+	2	1740	c.1021C>T	c.(1021-1023)CGG>TGG	p.R341W		NM_003412	NP_003403	Q15915	ZIC1_HUMAN	zinc finger protein of the cerebellum 1	341	C2H2-type 4.				behavior|brain development|cell differentiation|inner ear morphogenesis|pattern specification process|positive regulation of protein import into nucleus|positive regulation of transcription, DNA-dependent|regulation of smoothened signaling pathway	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
TM4SF18	116441	broad.mit.edu	37	3	149040176	149040176	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149040176T>G	uc003exa.2	-	5	595	c.458A>C	c.(457-459)CAT>CCT	p.H153P		NM_138786	NP_620141	Q96CE8	T4S18_HUMAN	transmembrane 4 L six family member 18	153	Extracellular (Potential).					integral to membrane				ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)															---	---	---	---
RNF13	11342	broad.mit.edu	37	3	149629814	149629814	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149629814C>A	uc003exn.3	+	8	1334	c.550C>A	c.(550-552)CTA>ATA	p.L184I	RNF13_uc003exp.3_Missense_Mutation_p.L184I|RNF13_uc010hvh.2_Missense_Mutation_p.L65I	NM_007282	NP_009213	O43567	RNF13_HUMAN	ring finger protein 13	184	Helical; (Potential).				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)															---	---	---	---
FAM194A	131831	broad.mit.edu	37	3	150387162	150387162	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150387162T>C	uc003eyg.2	-	12	1477	c.1420A>G	c.(1420-1422)ATG>GTG	p.M474V	FAM194A_uc003eyh.2_Missense_Mutation_p.M328V	NM_152394	NP_689607	Q7L0X2	F194A_HUMAN	hypothetical protein LOC131831	474										skin(2)|ovary(1)	3																		---	---	---	---
IGSF10	285313	broad.mit.edu	37	3	151155256	151155256	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151155256G>T	uc011bod.1	-	6	7093	c.7093C>A	c.(7093-7095)CCA>ACA	p.P2365T	IGSF10_uc011bob.1_Missense_Mutation_p.P392T|IGSF10_uc011boc.1_Missense_Mutation_p.P344T	NM_178822	NP_849144	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10 precursor	2365	Ig-like C2-type 10.				cell differentiation|multicellular organismal development|ossification	extracellular region				skin(7)|ovary(5)|central_nervous_system(1)	13			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)															---	---	---	---
IGSF10	285313	broad.mit.edu	37	3	151165105	151165105	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151165105T>G	uc011bod.1	-	4	2664	c.2664A>C	c.(2662-2664)CAA>CAC	p.Q888H		NM_178822	NP_849144	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10 precursor	888					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)															---	---	---	---
MFSD1	64747	broad.mit.edu	37	3	158541249	158541249	+	Silent	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158541249C>A	uc003fcl.1	+	12	1140	c.1110C>A	c.(1108-1110)GCC>GCA	p.A370A	MFSD1_uc003fcm.1_RNA|MFSD1_uc003fcn.1_Silent_p.A273A|MFSD1_uc011bow.1_Silent_p.A331A|MFSD1_uc011box.1_Silent_p.A297A	NM_022736	NP_073573	Q9H3U5	MFSD1_HUMAN	major facilitator superfamily domain containing	370	Helical; (Potential).				transmembrane transport	integral to membrane					0			Lung(72;0.00372)|LUSC - Lung squamous cell carcinoma(72;0.00523)															---	---	---	---
SI	6476	broad.mit.edu	37	3	164735863	164735863	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164735863C>T	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)			---	---	---	---
MECOM	2122	broad.mit.edu	37	3	168812977	168812977	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168812977C>T	uc003ffi.3	-	12	2611	c.2342G>A	c.(2341-2343)CGC>CAC	p.R781H	MECOM_uc010hwk.1_Missense_Mutation_p.R795H|MECOM_uc003ffj.3_Missense_Mutation_p.R846H|MECOM_uc011bpi.1_Missense_Mutation_p.R773H|MECOM_uc003ffn.3_Missense_Mutation_p.R781H|MECOM_uc003ffk.2_Missense_Mutation_p.R772H|MECOM_uc003ffl.2_Missense_Mutation_p.R932H|MECOM_uc011bpj.1_Missense_Mutation_p.R969H|MECOM_uc011bpk.1_Missense_Mutation_p.R771H	NM_005241	NP_005232	Q03112	EVI1_HUMAN	MDS1 and EVI1 complex locus isoform b	781	C2H2-type 9.				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																		---	---	---	---
SKIL	6498	broad.mit.edu	37	3	170078921	170078921	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170078921T>C	uc003fgu.2	+	2	1514	c.802T>C	c.(802-804)TGC>CGC	p.C268R	SKIL_uc011bps.1_Missense_Mutation_p.C248R|SKIL_uc003fgv.2_Missense_Mutation_p.C268R|SKIL_uc003fgw.2_Missense_Mutation_p.C268R	NM_005414	NP_005405	P12757	SKIL_HUMAN	SKI-like isoform 1	268					cell cycle arrest|negative regulation of cell differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of axonogenesis|protein heterotrimerization|protein homotrimerization|regulation of apoptosis|regulation of apoptosis|response to antibiotic|response to growth factor stimulus|skeletal muscle tissue development	cytoplasm|PML body	chromatin binding|nucleotide binding|protein complex binding|protein domain specific binding|SMAD binding|transcription corepressor activity|transcription repressor activity			ovary(2)|skin(1)	3	all_cancers(22;7.13e-23)|all_epithelial(15;9.95e-28)|all_lung(20;1.23e-16)|Lung NSC(18;5.15e-16)|Ovarian(172;0.000337)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)															---	---	---	---
NCEH1	57552	broad.mit.edu	37	3	172365822	172365822	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172365822G>A	uc011bpx.1	-	2	455	c.317C>T	c.(316-318)GCG>GTG	p.A106V	NCEH1_uc003fig.2_Missense_Mutation_p.A106V|NCEH1_uc011bpw.1_5'UTR|NCEH1_uc011bpy.1_Intron	NM_001146276	NP_001139748	Q6PIU2	NCEH1_HUMAN	arylacetamide deacetylase-like 1 isoform a	74	Lumenal (Potential).				lipid catabolic process	endoplasmic reticulum|integral to membrane|microsome	carboxylesterase activity				0																		---	---	---	---
NAALADL2	254827	broad.mit.edu	37	3	174974288	174974288	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174974288T>C	uc003fit.2	+	4	995	c.908T>C	c.(907-909)CTG>CCG	p.L303P	NAALADL2_uc003fiu.1_Missense_Mutation_p.L296P|NAALADL2_uc010hwy.1_Missense_Mutation_p.L125P|NAALADL2_uc010hwz.1_5'UTR	NM_207015	NP_996898	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	303	Extracellular (Potential).				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)														---	---	---	---
MFN1	55669	broad.mit.edu	37	3	179103460	179103460	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179103460C>T	uc003fjs.2	+	15	1892	c.1766C>T	c.(1765-1767)GCG>GTG	p.A589V	MFN1_uc010hxb.2_RNA|MFN1_uc003fjt.2_Missense_Mutation_p.A617V|MFN1_uc010hxc.2_Missense_Mutation_p.A331V	NM_033540	NP_284941	Q8IWA4	MFN1_HUMAN	mitofusin 1	589	Helical; Name=1; (Potential).				mitochondrial fusion	integral to membrane|mitochondrial outer membrane	GTP binding|GTPase activity			ovary(2)|large_intestine(1)	3	all_cancers(143;1.67e-16)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.00225)|BRCA - Breast invasive adenocarcinoma(182;0.0923)															---	---	---	---
TTC14	151613	broad.mit.edu	37	3	180320042	180320042	+	5'UTR	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180320042C>T	uc003fkk.2	+	1					TTC14_uc003fkl.2_5'UTR|TTC14_uc003fkm.2_5'UTR	NM_133462	NP_597719			tetratricopeptide repeat domain 14 isoform a								RNA binding			ovary(1)	1	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)															---	---	---	---
AP2M1	1173	broad.mit.edu	37	3	183901344	183901344	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183901344T>C	uc011bqx.1	+	12	1405	c.1248T>C	c.(1246-1248)CAT>CAC	p.H416H	AP2M1_uc003fmw.2_Silent_p.H414H|AP2M1_uc003fmx.2_Silent_p.H344H|AP2M1_uc003fmy.2_Silent_p.H414H|AP2M1_uc011bqy.1_Silent_p.H286H|ABCF3_uc003fmz.2_5'Flank|ABCF3_uc003fna.2_5'Flank	NM_004068	NP_004059	Q96CW1	AP2M1_HUMAN	adaptor-related protein complex 2, mu 1 subunit	416	MHD.				axon guidance|cellular membrane organization|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|vesicle-mediated transport|viral reproduction	clathrin adaptor complex|clathrin coat of coated pit|cytosol|endocytic vesicle membrane|peroxisomal membrane	lipid binding|protein binding|transporter activity				0	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.92e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)															---	---	---	---
ECE2	9718	broad.mit.edu	37	3	183996007	183996007	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183996007T>C	uc003fni.3	+	6	1048	c.1010T>C	c.(1009-1011)GTG>GCG	p.V337A	ECE2_uc011brg.1_Missense_Mutation_p.V265A|ECE2_uc011brh.1_Missense_Mutation_p.V190A|ECE2_uc003fnl.3_Missense_Mutation_p.V265A|ECE2_uc003fnm.3_Missense_Mutation_p.V219A|ECE2_uc003fnk.3_Missense_Mutation_p.V190A|ECE2_uc011bri.1_Missense_Mutation_p.V252A|ECE2_uc010hxv.2_Missense_Mutation_p.V3A	NM_014693	NP_055508	O60344	ECE2_HUMAN	endothelin converting enzyme 2 isoform A	337	Lumenal (Potential).|Endothelin-converting enzyme 2 region.				brain development|cardioblast differentiation|cell-cell signaling|peptide hormone processing	cytoplasmic vesicle membrane|Golgi membrane|integral to membrane	metal ion binding|metalloendopeptidase activity|methyltransferase activity			ovary(2)|skin(2)	4	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)															---	---	---	---
EPHB3	2049	broad.mit.edu	37	3	184290720	184290720	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184290720C>T	uc003foz.2	+	3	1049	c.612C>T	c.(610-612)TCC>TCT	p.S204S		NM_004443	NP_004434	P54753	EPHB3_HUMAN	ephrin receptor EphB3 precursor	204	Cys-rich.|Extracellular (Potential).					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)															---	---	---	---
MASP1	5648	broad.mit.edu	37	3	186943127	186943127	+	Nonsense_Mutation	SNP	C	A	A	rs140787141		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186943127C>A	uc003frh.1	-	13	2058	c.1726G>T	c.(1726-1728)GGA>TGA	p.G576*		NM_001879	NP_001870	P48740	MASP1_HUMAN	mannan-binding lectin serine protease 1 isoform	576	Peptidase S1.				complement activation, lectin pathway|negative regulation of complement activation|proteolysis	extracellular space	calcium ion binding|calcium-dependent protein binding|protein binding|protein homodimerization activity|serine-type endopeptidase activity			ovary(2)|breast(1)|liver(1)	4	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)														---	---	---	---
ATP13A4	84239	broad.mit.edu	37	3	193220365	193220365	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193220365C>T	uc003ftd.2	-	3	406	c.298G>A	c.(298-300)GCA>ACA	p.A100T	ATP13A4_uc003fte.1_Missense_Mutation_p.A100T|ATP13A4_uc011bsr.1_5'UTR	NM_032279	NP_115655	Q4VNC1	AT134_HUMAN	ATPase type 13A4	100	Extracellular (Potential).				ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(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)														---	---	---	---
LRRC33	375387	broad.mit.edu	37	3	196386683	196386683	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196386683C>T	uc003fwv.2	+	3	273	c.169C>T	c.(169-171)CCC>TCC	p.P57S		NM_198565	NP_940967	Q86YC3	LRC33_HUMAN	leucine rich repeat containing 33 precursor	57	Extracellular (Potential).					integral to membrane				ovary(2)|central_nervous_system(1)	3	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.9e-23)|all cancers(36;1.76e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00326)														---	---	---	---
DLG1	1739	broad.mit.edu	37	3	196842851	196842851	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196842851C>T	uc003fxo.3	-	14	1679	c.1489G>A	c.(1489-1491)GGA>AGA	p.G497R	DLG1_uc011bub.1_Missense_Mutation_p.G381R|DLG1_uc011buc.1_Missense_Mutation_p.G381R|DLG1_uc011bud.1_Missense_Mutation_p.G180R|DLG1_uc003fxn.3_Missense_Mutation_p.G497R|DLG1_uc011bue.1_Missense_Mutation_p.G464R|DLG1_uc010ial.2_Missense_Mutation_p.G497R|DLG1_uc011buf.1_Intron|DLG1_uc003fxp.2_RNA|DLG1_uc010iam.1_Missense_Mutation_p.G464R|DLG1_uc010ian.2_Missense_Mutation_p.G364R	NM_001098424	NP_001091894	Q12959	DLG1_HUMAN	discs, large homolog 1 isoform 1	497	PDZ 3.				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)														---	---	---	---
PIGG	54872	broad.mit.edu	37	4	527699	527699	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:527699G>A	uc003gak.3	+	12	2800	c.2664G>A	c.(2662-2664)GCG>GCA	p.A888A	PIGG_uc003gaj.3_Silent_p.A880A|PIGG_uc011bux.1_RNA|PIGG_uc010ibf.2_Silent_p.A755A|PIGG_uc003gal.3_Silent_p.A799A	NM_001127178	NP_001120650	Q5H8A4	PIGG_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	888	Helical; (Potential).				C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	CP2 mannose-ethanolamine phosphotransferase activity			central_nervous_system(2)|ovary(1)|skin(1)	4																		---	---	---	---
GAK	2580	broad.mit.edu	37	4	870355	870355	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:870355A>C	uc003gbm.3	-	18	2216	c.2017T>G	c.(2017-2019)TTT>GTT	p.F673V	GAK_uc003gbn.3_Missense_Mutation_p.F594V|GAK_uc010ibk.1_Missense_Mutation_p.F567V|GAK_uc003gbl.3_Missense_Mutation_p.F537V	NM_005255	NP_005246	O14976	GAK_HUMAN	cyclin G associated kinase	673	C2 tensin-type.				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)														---	---	---	---
WHSC2	7469	broad.mit.edu	37	4	1993434	1993434	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1993434G>A	uc003gem.2	-	2	492	c.252C>T	c.(250-252)GGC>GGT	p.G84G	WHSC2_uc003gel.2_5'UTR|WHSC2_uc003gen.2_Intron	NM_005663	NP_005654	Q9H3P2	NELFA_HUMAN	Wolf-Hirschhorn syndrome candidate 2 protein	73					multicellular organismal development|positive regulation of viral transcription|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm				skin(1)	1			OV - Ovarian serous cystadenocarcinoma(23;0.0155)															---	---	---	---
TNIP2	79155	broad.mit.edu	37	4	2746112	2746112	+	Splice_Site	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2746112A>G	uc003gfg.2	-	5	1113	c.1026_splice	c.e5+1	p.Q342_splice	TNIP2_uc003gff.2_Splice_Site_p.Q235_splice|TNIP2_uc003gfh.2_Splice_Site_p.Q259_splice	NM_024309	NP_077285			A20-binding inhibitor of NF-kappaB activation 2							cytosol	protein binding			central_nervous_system(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
STX18	53407	broad.mit.edu	37	4	4421856	4421856	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4421856C>A	uc003gic.2	-	11	997	c.913G>T	c.(913-915)GCC>TCC	p.A305S		NM_016930	NP_058626	Q9P2W9	STX18_HUMAN	syntaxin 18	305	t-SNARE coiled-coil homology.|Cytoplasmic (Potential).				ER to Golgi vesicle-mediated transport|intracellular protein transport	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	SNAP receptor activity				0				UCEC - Uterine corpus endometrioid carcinoma (64;0.0534)														---	---	---	---
EVC2	132884	broad.mit.edu	37	4	5620413	5620413	+	Intron	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5620413G>A	uc003gij.2	-						EVC2_uc011bwb.1_Intron|EVC2_uc003gik.2_Intron	NM_147127	NP_667338			limbin							integral to membrane				large_intestine(3)|ovary(2)	5																		---	---	---	---
SH3TC1	54436	broad.mit.edu	37	4	8229435	8229435	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8229435G>A	uc003gkv.3	+	12	2115	c.2014G>A	c.(2014-2016)GCC>ACC	p.A672T	SH3TC1_uc003gkw.3_Missense_Mutation_p.A596T|SH3TC1_uc003gkx.3_RNA|SH3TC1_uc003gky.2_5'Flank	NM_018986	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	672	TPR 3.						binding			large_intestine(2)|pancreas(1)	3																		---	---	---	---
BOD1L	259282	broad.mit.edu	37	4	13610236	13610236	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13610236C>T	uc003gmz.1	-	8	1777	c.1660G>A	c.(1660-1662)GCC>ACC	p.A554T	BOD1L_uc010idr.1_5'UTR	NM_148894	NP_683692	Q8NFC6	BOD1L_HUMAN	biorientation of chromosomes in cell division	554	Lys-rich.						DNA binding			ovary(5)|breast(1)	6																		---	---	---	---
KLF3	51274	broad.mit.edu	37	4	38691506	38691506	+	Intron	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38691506T>C	uc003gth.3	+						KLF3_uc003gtg.2_3'UTR	NM_016531	NP_057615			Kruppel-like factor 3 (basic)						multicellular organismal development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)	2																		---	---	---	---
TLR1	7096	broad.mit.edu	37	4	38798205	38798205	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38798205T>C	uc003gtl.2	-	4	2522	c.2248A>G	c.(2248-2250)ATG>GTG	p.M750V		NM_003263	NP_003254	Q15399	TLR1_HUMAN	toll-like receptor 1 precursor	750	Cytoplasmic (Potential).|TIR.				cellular response to triacyl bacterial lipopeptide|detection of triacyl bacterial lipopeptide|inflammatory response|innate immune response|macrophage activation|positive regulation of interleukin-6 biosynthetic process|positive regulation of tumor necrosis factor biosynthetic process	integral to plasma membrane|phagocytic vesicle membrane|Toll-like receptor 1-Toll-like receptor 2 protein complex	protein heterodimerization activity|transmembrane receptor activity			lung(2)|skin(2)|prostate(1)	5																		---	---	---	---
TLR6	10333	broad.mit.edu	37	4	38828698	38828698	+	3'UTR	SNP	A	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38828698A>T	uc003gtm.2	-	1					TLR6_uc010ifg.1_3'UTR	NM_006068	NP_006059			toll-like receptor 6 precursor						activation of NF-kappaB-inducing kinase activity|cellular response to diacyl bacterial lipopeptide|defense response to bacterium|detection of diacyl bacterial lipopeptide|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-6 biosynthetic process|positive regulation of JUN kinase activity|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	integral to plasma membrane|phagocytic vesicle membrane	lipopeptide binding|transmembrane receptor activity			ovary(2)	2																		---	---	---	---
LIMCH1	22998	broad.mit.edu	37	4	41640983	41640983	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41640983G>A	uc003gvu.3	+	9	1024	c.970G>A	c.(970-972)GAG>AAG	p.E324K	LIMCH1_uc003gvv.3_Missense_Mutation_p.E324K|LIMCH1_uc003gvw.3_Missense_Mutation_p.E324K|LIMCH1_uc003gvx.3_Intron|LIMCH1_uc003gwe.3_Missense_Mutation_p.E324K|LIMCH1_uc003gvy.3_Intron|LIMCH1_uc003gwa.3_Missense_Mutation_p.E165K|LIMCH1_uc003gvz.3_Missense_Mutation_p.E709K|LIMCH1_uc011byu.1_Intron|LIMCH1_uc003gwc.3_Missense_Mutation_p.E170K|LIMCH1_uc003gwd.3_Intron|LIMCH1_uc011byv.1_Missense_Mutation_p.E75K	NM_014988	NP_055803	Q9UPQ0	LIMC1_HUMAN	LIM and calponin homology domains 1 isoform a	324					actomyosin structure organization		actin binding|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
SLC30A9	10463	broad.mit.edu	37	4	42065035	42065035	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42065035C>T	uc003gwl.2	+	11	1075	c.929C>T	c.(928-930)TCG>TTG	p.S310L	SLC30A9_uc011byx.1_Missense_Mutation_p.S70L	NM_006345	NP_006336	Q6PML9	ZNT9_HUMAN	solute carrier family 30 (zinc transporter),	310					nucleotide-excision repair|zinc ion transport	cytoskeleton|integral to membrane|nucleus	cation transmembrane transporter activity|nucleotide binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
ATP8A1	10396	broad.mit.edu	37	4	42466701	42466701	+	Intron	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42466701T>C	uc003gwr.2	-						ATP8A1_uc003gwq.2_Intron|ATP8A1_uc003gws.2_Intron	NM_006095	NP_006086			ATPase, aminophospholipid transporter (APLT),						ATP biosynthetic process	chromaffin granule membrane|integral to membrane|plasma membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			skin(2)|central_nervous_system(1)	3					Phosphatidylserine(DB00144)													---	---	---	---
GABRB1	2560	broad.mit.edu	37	4	47034506	47034506	+	Intron	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47034506G>A	uc003gxh.2	+						GABRB1_uc011bze.1_Intron|GABRB1_uc011bzd.1_Missense_Mutation_p.S82N|GABRB1_uc010igg.2_Intron	NM_000812	NP_000803			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			ovary(2)	2					Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)													---	---	---	---
GABRB1	2560	broad.mit.edu	37	4	47408866	47408866	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47408866G>T	uc003gxh.2	+	8	1377	c.1003G>T	c.(1003-1005)GGC>TGC	p.G335C	GABRB1_uc011bze.1_Missense_Mutation_p.G265C	NM_000812	NP_000803	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta	335	Cytoplasmic (Probable).				synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)	2					Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)													---	---	---	---
NFXL1	152518	broad.mit.edu	37	4	47853912	47853912	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47853912A>G	uc010igh.2	-	21	2646	c.2469T>C	c.(2467-2469)TGT>TGC	p.C823C	NFXL1_uc003gxo.2_Silent_p.C148C|NFXL1_uc003gxp.2_Silent_p.C823C|NFXL1_uc003gxq.3_RNA|NFXL1_uc010igi.2_Silent_p.C823C	NM_152995	NP_694540	Q6ZNB6	NFXL1_HUMAN	nuclear transcription factor, X-box binding-like	823	Potential.					integral to membrane|nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
FRYL	285527	broad.mit.edu	37	4	48533267	48533267	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48533267G>A	uc003gyh.1	-	50	7414	c.6809C>T	c.(6808-6810)ACA>ATA	p.T2270I	FRYL_uc003gyg.1_Missense_Mutation_p.T966I|FRYL_uc003gyi.1_Missense_Mutation_p.T1158I|FRYL_uc003gyj.1_Missense_Mutation_p.T565I	NM_015030	NP_055845	O94915	FRYL_HUMAN	furry-like	2270					regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1																		---	---	---	---
OCIAD2	132299	broad.mit.edu	37	4	48901837	48901837	+	Intron	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48901837T>G	uc003gyt.2	-						OCIAD2_uc003gyu.2_Intron	NM_001014446	NP_001014446			OCIA domain containing 2 isoform 1							endosome					0																		---	---	---	---
RASL11B	65997	broad.mit.edu	37	4	53731797	53731797	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53731797A>G	uc003gzt.2	+	4	752	c.572A>G	c.(571-573)TAC>TGC	p.Y191C		NM_023940	NP_076429	Q9BPW5	RSLBB_HUMAN	RAS-like family 11 member B	191	Small GTPase-like.				small GTPase mediated signal transduction	membrane	GTP binding|GTPase activity			central_nervous_system(1)	1			LUSC - Lung squamous cell carcinoma(32;0.0302)															---	---	---	---
KDR	3791	broad.mit.edu	37	4	55976873	55976873	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55976873G>A	uc003has.2	-	8	1341	c.1039C>T	c.(1039-1041)CGT>TGT	p.R347C	KDR_uc003hat.1_Missense_Mutation_p.R347C|KDR_uc011bzx.1_Missense_Mutation_p.R347C	NM_002253	NP_002244	P35968	VGFR2_HUMAN	kinase insert domain receptor precursor	347	Ig-like C2-type 4.|Extracellular (Potential).				angiogenesis|cell differentiation|interspecies interaction between organisms|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of focal adhesion assembly|positive regulation of positive chemotaxis|regulation of cell shape	integral to plasma membrane	ATP binding|growth factor binding|Hsp90 protein binding|integrin binding|receptor signaling protein tyrosine kinase activity|vascular endothelial growth factor receptor activity			lung(16)|soft_tissue(4)|central_nervous_system(4)|large_intestine(2)|stomach(2)|skin(2)|ovary(2)|kidney(1)	33	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Sorafenib(DB00398)|Sunitinib(DB01268)			Mis		NSCLC|angiosarcoma				Familial_Infantile_Hemangioma	TSP Lung(20;0.16)			---	---	---	---
SRD5A3	79644	broad.mit.edu	37	4	56225642	56225642	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56225642G>A	uc003hau.2	+	2	446	c.351G>A	c.(349-351)GCG>GCA	p.A117A		NM_024592	NP_078868	Q9H8P0	PORED_HUMAN	steroid 5 alpha-reductase 3	117	Cytoplasmic (Potential).				androgen biosynthetic process|dolichol metabolic process|dolichol-linked oligosaccharide biosynthetic process|polyprenol catabolic process	endoplasmic reticulum membrane|integral to membrane	3-oxo-5-alpha-steroid 4-dehydrogenase activity|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor				0	all_cancers(7;0.0308)|all_lung(4;0.00195)|Lung NSC(11;0.00431)|all_epithelial(27;0.0425)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.0179)															---	---	---	---
NMU	10874	broad.mit.edu	37	4	56471486	56471486	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56471486C>A	uc003hbc.2	-	7	497	c.391G>T	c.(391-393)GTT>TTT	p.V131F	NMU_uc003hbd.1_Intron|NMU_uc010igv.1_RNA|NMU_uc010igw.1_Missense_Mutation_p.V46F|NMU_uc010igx.1_Intron	NM_006681	NP_006672	P48645	NMU_HUMAN	neuromedin U precursor	131					neuropeptide signaling pathway	extracellular region					0	Lung NSC(11;0.00256)|all_epithelial(27;0.075)|Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.103)	LUSC - Lung squamous cell carcinoma(4;6.72e-08)|Lung(4;6.22e-07)|Epithelial(7;0.00559)	LUSC - Lung squamous cell carcinoma(721;0.0115)														---	---	---	---
KIAA1211	57482	broad.mit.edu	37	4	57176872	57176872	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57176872C>A	uc003hbk.2	+	6	717	c.326C>A	c.(325-327)CCT>CAT	p.P109H	KIAA1211_uc010iha.2_Missense_Mutation_p.P102H|KIAA1211_uc011bzz.1_Missense_Mutation_p.P19H|KIAA1211_uc003hbl.2_RNA|KIAA1211_uc003hbm.1_Translation_Start_Site	NM_020722	NP_065773	Q6ZU35	K1211_HUMAN	hypothetical protein LOC57482	109										ovary(1)|skin(1)	2	Glioma(25;0.08)|all_neural(26;0.101)																	---	---	---	---
REST	5978	broad.mit.edu	37	4	57798315	57798315	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57798315G>A	uc003hch.2	+	4	3638	c.3291G>A	c.(3289-3291)GAG>GAA	p.E1097E	REST_uc003hci.2_Silent_p.E1097E|REST_uc010ihf.2_Silent_p.E771E	NM_005612	NP_005603	Q13127	REST_HUMAN	RE1-silencing transcription factor	1097					cardiac muscle cell myoblast differentiation|cellular response to drug|cellular response to electrical stimulus|cellular response to glucocorticoid stimulus|histone H4 deacetylation|negative regulation by host of viral transcription|negative regulation of aldosterone biosynthetic process|negative regulation of calcium ion-dependent exocytosis|negative regulation of cell proliferation|negative regulation of cortisol biosynthetic process|negative regulation of dense core granule biogenesis|negative regulation of insulin secretion|negative regulation of mesenchymal stem cell differentiation|negative regulation of neurogenesis|negative regulation of neuron differentiation|positive regulation of apoptosis|positive regulation of caspase activity|positive regulation of transcription, DNA-dependent	cytoplasm|transcriptional repressor complex	calcium channel activity|chromatin binding|core promoter proximal region sequence-specific DNA binding|core promoter sequence-specific DNA binding|outward rectifier potassium channel activity|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|zinc ion binding			skin(5)|upper_aerodigestive_tract(1)|ovary(1)|lung(1)|central_nervous_system(1)	9	Glioma(25;0.08)|all_neural(26;0.181)																	---	---	---	---
TECRL	253017	broad.mit.edu	37	4	65155489	65155489	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:65155489C>T	uc003hcv.2	-							NM_001010874	NP_001010874			steroid 5 alpha-reductase 2-like 2						lipid metabolic process	cytoplasm|integral to membrane	oxidoreductase activity, acting on the CH-CH group of donors				0																		---	---	---	---
UGT2B7	7364	broad.mit.edu	37	4	69962448	69962448	+	Silent	SNP	C	T	T	rs151180306		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69962448C>T	uc003heg.3	+	1	256	c.210C>T	c.(208-210)TCC>TCT	p.S70S	UGT2B7_uc010ihq.2_Silent_p.S70S	NM_001074	NP_001065	P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2B7 precursor	70					lipid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			ovary(1)|skin(1)	2																		---	---	---	---
C4orf35	85438	broad.mit.edu	37	4	71201725	71201725	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71201725C>T	uc003hff.2	+	1	1055	c.969C>T	c.(967-969)TTC>TTT	p.F323F		NM_033122	NP_149113	Q96KC9	CABS1_HUMAN	testis development protein NYD-SP26	323						flagellum	calcium ion binding				0		all_hematologic(202;0.196)																---	---	---	---
CDKL2	8999	broad.mit.edu	37	4	76507095	76507095	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76507095G>T	uc003hiq.2	-	11	1955	c.1430C>A	c.(1429-1431)CCC>CAC	p.P477H	CDKL2_uc011cbp.1_Missense_Mutation_p.P554H	NM_003948	NP_003939	Q92772	CDKL2_HUMAN	cyclin-dependent kinase-like 2	477					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)															---	---	---	---
USO1	8615	broad.mit.edu	37	4	76670540	76670540	+	Intron	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76670540G>T	uc003hiu.2	+							NM_003715	NP_003706			USO1 homolog, vesicle docking protein						intracellular protein transport|vesicle fusion with Golgi apparatus	cytosol|Golgi membrane	protein binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)															---	---	---	---
NAAA	27163	broad.mit.edu	37	4	76842184	76842184	+	Silent	SNP	C	T	T	rs141023635	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76842184C>T	uc003hjb.2	-	6	823	c.759G>A	c.(757-759)ACG>ACA	p.T253T	NAAA_uc003hja.2_Silent_p.T253T|NAAA_uc003hjc.3_Silent_p.T253T|NAAA_uc003hjd.3_RNA|NAAA_uc011cbq.1_Silent_p.T152T	NM_014435	NP_055250	Q02083	NAAA_HUMAN	N-acylethanolamine acid amidase isoform 1	253					lipid metabolic process	lysosome	hydrolase activity			skin(1)	1																		---	---	---	---
PAQR3	152559	broad.mit.edu	37	4	79856351	79856351	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79856351A>G	uc003hlp.1	-	2	476	c.272T>C	c.(271-273)ATG>ACG	p.M91T	PAQR3_uc003hlm.2_RNA|PAQR3_uc003hln.2_Intron|PAQR3_uc003hlq.1_Intron	NM_001040202	NP_001035292	Q6TCH7	PAQR3_HUMAN	progestin and adipoQ receptor family member III	91	Helical; (Potential).					Golgi membrane|integral to membrane	receptor activity				0																		---	---	---	---
HELQ	113510	broad.mit.edu	37	4	84369935	84369935	+	Splice_Site	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84369935C>T	uc003hom.2	-	3	1370	c.1191_splice	c.e3+1	p.K397_splice	HELQ_uc010ikb.2_Splice_Site_p.K397_splice|HELQ_uc003hol.3_Splice_Site|HELQ_uc010ikc.2_Splice_Site	NM_133636	NP_598375			DNA helicase HEL308								ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(1)|breast(1)|skin(1)	3													Direct_reversal_of_damage|Other_identified_genes_with_known_or_suspected_DNA_repair_function					---	---	---	---
WDFY3	23001	broad.mit.edu	37	4	85642585	85642585	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85642585G>A	uc003hpd.2	-	47	7990	c.7582C>T	c.(7582-7584)CGC>TGC	p.R2528C	WDFY3_uc003hpe.1_Missense_Mutation_p.R139C	NM_014991	NP_055806	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3 isoform	2528						cytoplasmic part|extrinsic to membrane|nuclear envelope	1-phosphatidylinositol binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)														---	---	---	---
PTPN13	5783	broad.mit.edu	37	4	87729029	87729029	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87729029A>G	uc003hpz.2	+	45	7542	c.7062A>G	c.(7060-7062)GCA>GCG	p.A2354A	PTPN13_uc003hpy.2_Silent_p.A2359A|PTPN13_uc003hqa.2_Silent_p.A2335A|PTPN13_uc003hqb.2_Silent_p.A2163A	NM_080683	NP_542414	Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type	2354	Tyrosine-protein phosphatase.					cytoplasm|cytoskeleton|plasma membrane	protein binding|protein binding|protein tyrosine phosphatase activity			ovary(4)|breast(1)|kidney(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)														---	---	---	---
AFF1	4299	broad.mit.edu	37	4	88029430	88029430	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88029430G>T	uc003hqj.3	+	10	1882	c.1475G>T	c.(1474-1476)AGC>ATC	p.S492I	AFF1_uc011ccz.1_Missense_Mutation_p.S499I|AFF1_uc003hqk.3_Missense_Mutation_p.S492I|AFF1_uc011cda.1_Missense_Mutation_p.S130I	NM_005935	NP_005926	P51825	AFF1_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	492	Poly-Ser.					nucleus	sequence-specific DNA binding transcription factor activity			breast(1)	1		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)														---	---	---	---
NUDT9	53343	broad.mit.edu	37	4	88370294	88370294	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88370294A>G	uc003hqq.2	+	5	854	c.531A>G	c.(529-531)AGA>AGG	p.R177R	NUDT9_uc003hqr.2_Silent_p.R127R|NUDT9_uc010ikl.2_Silent_p.R145R	NM_024047	NP_076952	Q9BW91	NUDT9_HUMAN	nudix-type motif 9 isoform a	177						mitochondrion	ADP-ribose diphosphatase activity				0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000937)														---	---	---	---
MMRN1	22915	broad.mit.edu	37	4	90856795	90856795	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90856795A>G	uc003hst.2	+	6	2035	c.1964A>G	c.(1963-1965)CAG>CGG	p.Q655R	MMRN1_uc010iku.2_Intron|MMRN1_uc011cds.1_Missense_Mutation_p.Q397R	NM_007351	NP_031377	Q13201	MMRN1_HUMAN	multimerin 1	655					cell adhesion|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen				ovary(4)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)														---	---	---	---
FAM190A	401145	broad.mit.edu	37	4	91230628	91230628	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91230628A>C	uc003hsv.3	+	2	1533	c.1193A>C	c.(1192-1194)GAG>GCG	p.E398A	FAM190A_uc003hsu.3_Missense_Mutation_p.E398A|FAM190A_uc010ikv.2_RNA|FAM190A_uc003hsw.2_Missense_Mutation_p.E398A	NM_001145065	NP_001138537	Q9C0I3	F190A_HUMAN	KIAA1680 protein isoform 1	398										large_intestine(1)|ovary(1)	2																		---	---	---	---
NHEDC2	133308	broad.mit.edu	37	4	103970157	103970157	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103970157G>A	uc003hwx.3	-	6	1478	c.606C>T	c.(604-606)GGC>GGT	p.G202G	NHEDC2_uc010iln.1_Silent_p.G54G|NHEDC2_uc003hwy.2_Silent_p.G202G|NHEDC2_uc011cew.1_Silent_p.G145G|NHEDC2_uc011cex.1_Silent_p.G145G|NHEDC2_uc011cey.1_Silent_p.G145G	NM_178833	NP_849155	Q86UD5	NHDC2_HUMAN	Na+/H+ exchanger domain containing 2	202					sodium ion transport	integral to membrane|mitochondrial membrane	solute:hydrogen antiporter activity				0				OV - Ovarian serous cystadenocarcinoma(123;2.3e-08)														---	---	---	---
CXXC4	80319	broad.mit.edu	37	4	105412257	105412257	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:105412257T>C	uc003hxg.2	-	1	211	c.196A>G	c.(196-198)ACT>GCT	p.T66A	uc003hxh.1_Intron|CXXC4_uc010ilo.2_Intron	NM_025212	NP_079488	Q9H2H0	CXXC4_HUMAN	CXXC finger 4	66					negative regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway|zygotic specification of dorsal/ventral axis		DNA binding|PDZ domain binding|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(123;3.05e-08)														---	---	---	---
LEF1	51176	broad.mit.edu	37	4	109088861	109088861	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109088861G>A	uc003hyt.1	-	1	718	c.63C>T	c.(61-63)GAC>GAT	p.D21D	LEF1_uc011cfj.1_5'Flank|LEF1_uc011cfk.1_5'Flank|LEF1_uc003hyu.1_Silent_p.D21D|LEF1_uc003hyv.1_Silent_p.D21D|LEF1_uc010imb.1_RNA	NM_016269	NP_057353	Q9UJU2	LEF1_HUMAN	lymphoid enhancer-binding factor 1 isoform 1	21	CTNNB1-binding (By similarity).|Asp/Glu-rich (acidic).				canonical Wnt receptor signaling pathway|cell chemotaxis|cellular response to interleukin-4|epithelial to mesenchymal transition|histone H3 acetylation|histone H4 acetylation|negative regulation of apoptosis in bone marrow|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cell-cell adhesion|negative regulation of DNA binding|negative regulation of estrogen receptor binding|negative regulation of interleukin-13 production|negative regulation of interleukin-4 production|negative regulation of interleukin-5 production|negative regulation of transcription, DNA-dependent|neutrophil differentiation|osteoblast differentiation|palate development|positive regulation by host of viral transcription|positive regulation of cell cycle process|positive regulation of cell growth|positive regulation of cell migration|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of cell proliferation in bone marrow|positive regulation of cell-cell adhesion|positive regulation of epithelial to mesenchymal transition|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|T-helper 1 cell differentiation	cytoplasm|protein-DNA complex|transcription factor complex	armadillo repeat domain binding|beta-catenin binding|C2H2 zinc finger domain binding|caspase inhibitor activity|DNA bending activity|enhancer binding|estrogen receptor activity|estrogen receptor binding|gamma-catenin binding|histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding			large_intestine(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.000224)														---	---	---	---
EGF	1950	broad.mit.edu	37	4	110916038	110916038	+	Splice_Site	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110916038T>C	uc003hzy.3	+	20	3457	c.3005_splice	c.e20+2	p.N1002_splice	EGF_uc011cfu.1_Splice_Site_p.N960_splice|EGF_uc011cfv.1_Splice_Site_p.N961_splice|EGF_uc010imk.2_Splice_Site_p.N150_splice	NM_001963	NP_001954			epidermal growth factor precursor						angiogenesis|DNA replication|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of secretion|platelet activation|platelet degranulation|positive regulation of catenin import into nucleus|positive regulation of epidermal growth factor receptor activity|positive regulation of MAP kinase activity|positive regulation of mitosis|regulation of calcium ion import|regulation of protein localization at cell surface	integral to membrane|plasma membrane|platelet alpha granule lumen	calcium ion binding|epidermal growth factor receptor binding|growth factor activity|transmembrane receptor protein tyrosine kinase activator activity			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sulindac(DB00605)													---	---	---	---
PRSS12	8492	broad.mit.edu	37	4	119252889	119252889	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119252889C>T	uc003ica.1	-	4	1000	c.953G>A	c.(952-954)TGC>TAC	p.C318Y		NM_003619	NP_003610	P56730	NETR_HUMAN	neurotrypsin precursor	318	SRCR 2.					membrane	scavenger receptor activity			skin(1)	1																		---	---	---	---
TRPC3	7222	broad.mit.edu	37	4	122853717	122853717	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122853717C>T	uc003ieg.2	-	2	770	c.696G>A	c.(694-696)CCG>CCA	p.P232P	TRPC3_uc010inr.2_Silent_p.P159P|TRPC3_uc003ief.2_Silent_p.P159P|TRPC3_uc011cgl.1_5'UTR	NM_001130698	NP_001124170	Q13507	TRPC3_HUMAN	transient receptor potential cation channel,	147	Cytoplasmic (Potential).|ANK 4.				axon guidance|phototransduction|platelet activation	integral to plasma membrane	protein binding|store-operated calcium channel activity			ovary(2)	2																		---	---	---	---
KIAA1109	84162	broad.mit.edu	37	4	123229236	123229236	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123229236C>T	uc003ieh.2	+	56	10019	c.9974C>T	c.(9973-9975)GCC>GTC	p.A3325V	KIAA1109_uc003iel.1_Missense_Mutation_p.A1260V	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein	3325					regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12																		---	---	---	---
ANKRD50	57182	broad.mit.edu	37	4	125590323	125590323	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125590323T>C	uc003ifg.3	-	3	4375	c.4109A>G	c.(4108-4110)CAG>CGG	p.Q1370R	ANKRD50_uc011cgo.1_Missense_Mutation_p.Q1191R|ANKRD50_uc010inw.2_Missense_Mutation_p.Q1370R	NM_020337	NP_065070	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	1370										central_nervous_system(1)	1																		---	---	---	---
FAT4	79633	broad.mit.edu	37	4	126373398	126373398	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126373398G>T	uc003ifj.3	+	9	11227	c.11227G>T	c.(11227-11229)GGC>TGC	p.G3743C	FAT4_uc011cgp.1_Missense_Mutation_p.G2041C|FAT4_uc003ifi.1_Missense_Mutation_p.G1221C	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	3743	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	126411502	126411502	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126411502G>A	uc003ifj.3	+	17	13525	c.13525G>A	c.(13525-13527)GTG>ATG	p.V4509M	FAT4_uc011cgp.1_Missense_Mutation_p.V2750M|FAT4_uc003ifi.1_Missense_Mutation_p.V1986M	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	4509	Helical; (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	134071539	134071539	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134071539G>A	uc003iha.2	+	1	1070	c.244G>A	c.(244-246)GAA>AAA	p.E82K	uc003igy.2_5'Flank|PCDH10_uc003igz.2_Missense_Mutation_p.E82K	NM_032961	NP_116586	Q9P2E7	PCD10_HUMAN	protocadherin 10 isoform 1 precursor	82	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)														---	---	---	---
PCDH18	54510	broad.mit.edu	37	4	138442404	138442404	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:138442404G>A	uc003ihe.3	-	4	3574	c.3187C>T	c.(3187-3189)CAA>TAA	p.Q1063*	PCDH18_uc003ihf.3_Nonsense_Mutation_p.Q1055*|PCDH18_uc011cgz.1_Nonsense_Mutation_p.Q274*|PCDH18_uc003ihg.3_Nonsense_Mutation_p.Q842*|PCDH18_uc011cha.1_Nonsense_Mutation_p.Q243*	NM_019035	NP_061908	Q9HCL0	PCD18_HUMAN	protocadherin 18 precursor	1063	Interaction with DAB1 (By similarity).|Cytoplasmic (Potential).				brain development|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			pancreas(3)|skin(2)	5	all_hematologic(180;0.24)																	---	---	---	---
INPP4B	8821	broad.mit.edu	37	4	143033722	143033722	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143033722A>T	uc003iix.3	-	23	2844	c.2249T>A	c.(2248-2250)ATC>AAC	p.I750N	INPP4B_uc003iiw.3_Missense_Mutation_p.I750N|INPP4B_uc011chm.1_RNA|INPP4B_uc011chn.1_Missense_Mutation_p.I565N|INPP4B_uc011cho.1_RNA	NM_003866	NP_003857	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II,	750					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)																	---	---	---	---
SLC10A7	84068	broad.mit.edu	37	4	147431088	147431088	+	Silent	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147431088G>T	uc010ioz.2	-	3	551	c.297C>A	c.(295-297)CCC>CCA	p.P99P	SLC10A7_uc003ikr.2_Silent_p.P99P|SLC10A7_uc010ipa.2_Silent_p.P99P|SLC10A7_uc003iks.2_RNA|SLC10A7_uc003ikt.2_Silent_p.P99P	NM_001029998	NP_001025169	Q0GE19	NTCP7_HUMAN	solute carrier family 10 (sodium/bile acid	99						integral to membrane	bile acid:sodium symporter activity				0	all_hematologic(180;0.151)																	---	---	---	---
NR3C2	4306	broad.mit.edu	37	4	149357363	149357363	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149357363G>A	uc003ilj.3	-	2	984	c.650C>T	c.(649-651)ACA>ATA	p.T217I	NR3C2_uc003ilk.3_Missense_Mutation_p.T217I|NR3C2_uc010iph.2_RNA	NM_000901	NP_000892	P08235	MCR_HUMAN	nuclear receptor subfamily 3, group C, member 2	217	Modulating.				regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	endoplasmic reticulum membrane|nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding			large_intestine(1)	1	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0614)	Desoxycorticosterone Pivalate(DB01134)|Eplerenone(DB00700)|Fludrocortisone(DB00687)|Spironolactone(DB00421)													---	---	---	---
PET112L	5188	broad.mit.edu	37	4	152629159	152629159	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152629159C>T	uc003iml.2	-	6	870	c.858G>A	c.(856-858)AGG>AGA	p.R286R	PET112L_uc003imm.3_Silent_p.R286R	NM_004564	NP_004555	O75879	GATB_HUMAN	PET112-like precursor	286						mitochondrion	ATP binding|carbon-nitrogen ligase activity, with glutamine as amido-N-donor|translation factor activity, nucleic acid binding				0	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)			L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)													---	---	---	---
RNF175	285533	broad.mit.edu	37	4	154669938	154669938	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154669938G>A	uc003int.2	-	3	478	c.105C>T	c.(103-105)AAC>AAT	p.N35N	RNF175_uc003inu.1_5'UTR	NM_173662	NP_775933	Q8N4F7	RN175_HUMAN	ring finger protein 175	35						integral to membrane	zinc ion binding			ovary(1)|pancreas(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)																---	---	---	---
FGA	2243	broad.mit.edu	37	4	155505650	155505650	+	Silent	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155505650G>T	uc003iod.1	-	6	2285	c.2227C>A	c.(2227-2229)CGG>AGG	p.R743R		NM_000508	NP_000499	P02671	FIBA_HUMAN	fibrinogen, alpha polypeptide isoform alpha-E	743	Fibrinogen C-terminal.				platelet activation|platelet degranulation|protein polymerization|response to calcium ion|signal transduction	external side of plasma membrane|fibrinogen complex|platelet alpha granule lumen	eukaryotic cell surface binding|protein binding, bridging|receptor binding			ovary(2)|breast(1)	3	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)													---	---	---	---
FGG	2266	broad.mit.edu	37	4	155533542	155533542	+	Splice_Site	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155533542C>T	uc003ioj.2	-	2	264	c.123_splice	c.e2+1	p.F41_splice	FGG_uc003iog.2_Splice_Site_p.F41_splice|FGG_uc003ioh.2_Splice_Site_p.F41_splice|FGG_uc010ipx.2_Splice_Site|FGG_uc010ipy.2_Splice_Site|FGG_uc003ioi.2_5'Flank|FGG_uc003iok.2_Splice_Site_p.F41_splice	NM_021870	NP_068656			fibrinogen, gamma chain isoform gamma-B						platelet activation|platelet degranulation|protein polymerization|response to calcium ion|signal transduction	external side of plasma membrane|fibrinogen complex|platelet alpha granule lumen	eukaryotic cell surface binding|protein binding, bridging|receptor binding				0	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)													---	---	---	---
MAP9	79884	broad.mit.edu	37	4	156274447	156274447	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156274447A>G	uc003ios.2	-	11	1690	c.1426T>C	c.(1426-1428)TGG>CGG	p.W476R	MAP9_uc011cin.1_Missense_Mutation_p.W451R|MAP9_uc010iqa.1_RNA|MAP9_uc003iot.1_Missense_Mutation_p.W475R	NM_001039580	NP_001034669	Q49MG5	MAP9_HUMAN	aster-associated protein	476	Potential.				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)														---	---	---	---
RAPGEF2	9693	broad.mit.edu	37	4	160277155	160277155	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160277155G>A	uc003iqg.3	+	23	4629	c.4319G>A	c.(4318-4320)CGA>CAA	p.R1440Q		NM_014247	NP_055062	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor 2	1440					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)														---	---	---	---
FSTL5	56884	broad.mit.edu	37	4	162307082	162307082	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:162307082C>T	uc003iqh.2	-	16	2797	c.2361G>A	c.(2359-2361)AAG>AAA	p.K787K	FSTL5_uc003iqi.2_Silent_p.K786K|FSTL5_uc010iqv.2_Silent_p.K777K|uc010iqu.1_RNA	NM_020116	NP_064501	Q8N475	FSTL5_HUMAN	follistatin-like 5 isoform a	787						extracellular region	calcium ion binding			ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|skin(1)	8	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)														---	---	---	---
KLHL2	11275	broad.mit.edu	37	4	166220752	166220752	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166220752C>T	uc003irb.2	+	8	1124	c.865C>T	c.(865-867)CGT>TGT	p.R289C	KLHL2_uc011cjm.1_Missense_Mutation_p.R293C|KLHL2_uc003irc.2_Missense_Mutation_p.R201C|KLHL2_uc010ira.2_5'UTR	NM_007246	NP_009177	O95198	KLHL2_HUMAN	kelch-like 2, Mayven isoform 1	289					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)														---	---	---	---
HAND2	9464	broad.mit.edu	37	4	174450154	174450154	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174450154C>T	uc003ith.1	-	1	1225	c.287G>A	c.(286-288)CGC>CAC	p.R96H	NBLA00301_uc011ckd.1_5'Flank|NBLA00301_uc003itl.3_5'Flank|NBLA00301_uc003itj.2_5'Flank|NBLA00301_uc010irf.2_5'Flank|NBLA00301_uc010irg.2_5'Flank|NBLA00301_uc010irh.2_5'Flank|NBLA00301_uc010iri.2_5'Flank|NBLA00301_uc010irj.2_5'Flank|NBLA00301_uc010irk.2_5'Flank|NBLA00301_uc010irl.2_5'Flank|NBLA00301_uc010irm.2_5'Flank|NBLA00301_uc010irn.2_5'Flank|NBLA00301_uc003itk.2_5'Flank|HAND2_uc003itg.1_Intron|HAND2_uc010ire.1_Missense_Mutation_p.R96H	NM_021973	NP_068808	P61296	HAND2_HUMAN	basic helix-loop-helix transcription factor	96					adult heart development|angiogenesis|apoptosis|cardiac neural crest cell development involved in outflow tract morphogenesis|heart looping|in utero embryonic development|negative regulation of cardiac muscle cell apoptosis|noradrenergic neuron differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription regulatory region DNA binding|regulation of secondary heart field cardioblast proliferation|thymus development	nuclear chromatin|transcription factor complex	activating transcription factor binding|protein homodimerization activity|RNA polymerase II regulatory region sequence-specific DNA binding|transcription coactivator activity			skin(1)	1		Prostate(90;0.00601)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_neural(102;0.0837)|all_hematologic(60;0.107)		all cancers(43;1.37e-18)|Epithelial(43;5.5e-17)|OV - Ovarian serous cystadenocarcinoma(60;3.3e-10)|STAD - Stomach adenocarcinoma(60;0.00273)|GBM - Glioblastoma multiforme(59;0.0064)|LUSC - Lung squamous cell carcinoma(193;0.0903)|Kidney(143;0.249)														---	---	---	---
SLC9A3	6550	broad.mit.edu	37	5	488488	488488	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:488488G>A	uc003jbe.2	-	3	730	c.618C>T	c.(616-618)AAC>AAT	p.N206N	SLC9A3_uc011clx.1_Silent_p.N206N	NM_004174	NP_004165	P48764	SL9A3_HUMAN	solute carrier family 9 (sodium/hydrogen	206	Cytoplasmic (Potential).					cell surface|integral to membrane	sodium:hydrogen antiporter activity				0			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)															---	---	---	---
LPCAT1	79888	broad.mit.edu	37	5	1488543	1488543	+	Silent	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1488543A>C	uc003jcm.2	-	5	747	c.630T>G	c.(628-630)ACT>ACG	p.T210T		NM_024830	NP_079106	Q8NF37	PCAT1_HUMAN	lysophosphatidylcholine acyltransferase 1	210	Lumenal (Potential).				phospholipid biosynthetic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	1-acylglycerophosphocholine O-acyltransferase activity|1-alkylglycerophosphocholine O-acetyltransferase activity|calcium ion binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(19;0.0274)|all cancers(22;0.0534)	GBM - Glioblastoma multiforme(108;0.156)														---	---	---	---
MRPL36	64979	broad.mit.edu	37	5	1798838	1798838	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1798838A>G	uc003jcx.3	-	2	275	c.212T>C	c.(211-213)GTC>GCC	p.V71A	NDUFS6_uc003jcy.2_5'Flank	NM_032479	NP_115868	Q9P0J6	RM36_HUMAN	mitochondrial ribosomal protein L36 precursor	71					translation	mitochondrial large ribosomal subunit	structural constituent of ribosome				0				GBM - Glioblastoma multiforme(108;0.241)														---	---	---	---
IRX2	153572	broad.mit.edu	37	5	2749167	2749167	+	Splice_Site	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2749167C>A	uc003jda.2	-	3	898	c.656_splice	c.e3-1	p.G219_splice	IRX2_uc003jdb.2_Splice_Site_p.G219_splice	NM_001134222	NP_001127694			iroquois homeobox 2							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(1)	1				GBM - Glioblastoma multiforme(108;0.204)														---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14293236	14293236	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14293236A>G	uc003jff.2	+	6	1175	c.1169A>G	c.(1168-1170)AAC>AGC	p.N390S	TRIO_uc003jfg.2_RNA|TRIO_uc011cna.1_Missense_Mutation_p.N341S|TRIO_uc003jfh.1_Missense_Mutation_p.N39S	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)	390	Spectrin 1.				apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)																	---	---	---	---
TARS	6897	broad.mit.edu	37	5	33456321	33456321	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33456321A>G	uc003jhy.2	+	8	1121	c.826A>G	c.(826-828)AAA>GAA	p.K276E	TARS_uc011cob.1_Missense_Mutation_p.K264E|TARS_uc010iup.1_Missense_Mutation_p.K217E|TARS_uc011coc.1_Missense_Mutation_p.K297E|TARS_uc003jhz.2_Missense_Mutation_p.K172E|TARS_uc011cod.1_Missense_Mutation_p.K155E	NM_152295	NP_689508	P26639	SYTC_HUMAN	threonyl-tRNA synthetase	276					threonyl-tRNA aminoacylation	cytosol	ATP binding|protein homodimerization activity|threonine-tRNA ligase activity			ovary(2)	2					L-Threonine(DB00156)													---	---	---	---
NIPBL	25836	broad.mit.edu	37	5	37057423	37057423	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37057423T>A	uc003jkl.3	+	43	7898	c.7399T>A	c.(7399-7401)TCA>ACA	p.S2467T	NIPBL_uc003jkk.3_Missense_Mutation_p.S2467T|NIPBL_uc003jkn.2_Missense_Mutation_p.S160T	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A	2467					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)															---	---	---	---
DAB2	1601	broad.mit.edu	37	5	39390017	39390017	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39390017A>G	uc003jlx.2	-	6	1011	c.480T>C	c.(478-480)GTT>GTC	p.V160V	DAB2_uc003jlw.2_Silent_p.V160V	NM_001343	NP_001334	P98082	DAB2_HUMAN	disabled homolog 2	160	PID.				cell proliferation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of protein binding|negative regulation of transcription, DNA-dependent|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of transcription, DNA-dependent|positive regulation of Wnt receptor signaling pathway, planar cell polarity pathway	clathrin coated vesicle membrane|coated pit	protein C-terminus binding			kidney(2)|skin(1)	3	all_lung(31;0.000197)		Epithelial(62;0.137)															---	---	---	---
PRKAA1	5562	broad.mit.edu	37	5	40767726	40767726	+	Silent	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40767726T>G	uc003jmc.2	-	6	669	c.663A>C	c.(661-663)GGA>GGC	p.G221G	PRKAA1_uc003jmb.2_Silent_p.G236G	NM_006251	NP_006242	Q13131	AAPK1_HUMAN	protein kinase, AMP-activated, alpha 1 catalytic	221	Protein kinase.				activation of MAPK activity|cell cycle arrest|cholesterol biosynthetic process|fatty acid biosynthetic process|insulin receptor signaling pathway|negative regulation of glucosylceramide biosynthetic process|positive regulation of anti-apoptosis|positive regulation of cholesterol biosynthetic process|regulation of fatty acid oxidation|response to hypoxia	cytosol	ATP binding|cAMP-dependent protein kinase activity|metal ion binding|protein binding			breast(1)	1					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Phenformin(DB00914)													---	---	---	---
HEATR7B2	133558	broad.mit.edu	37	5	41012737	41012737	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41012737C>T	uc003jmj.3	-	30	3573	c.3083G>A	c.(3082-3084)GGC>GAC	p.G1028D	HEATR7B2_uc003jmi.3_Missense_Mutation_p.G583D	NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN	HEAT repeat family member 7B2	1028	HEAT 11.						binding			ovary(6)|central_nervous_system(2)	8																		---	---	---	---
NNT	23530	broad.mit.edu	37	5	43651871	43651871	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43651871A>G	uc003joe.2	+	13	2003	c.1748A>G	c.(1747-1749)GAC>GGC	p.D583G	NNT_uc003jof.2_Missense_Mutation_p.D583G	NM_012343	NP_036475	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	583	Mitochondrial matrix.				tricarboxylic acid cycle	integral to membrane|mitochondrial respiratory chain	NAD binding|NAD(P)+ transhydrogenase (AB-specific) activity|NAD(P)+ transhydrogenase (B-specific) activity|NADP binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(6;2.58e-06)				NADH(DB00157)													---	---	---	---
NNT	23530	broad.mit.edu	37	5	43700345	43700345	+	Intron	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43700345T>C	uc003joe.2	+						NNT_uc003jof.2_Intron	NM_012343	NP_036475			nicotinamide nucleotide transhydrogenase						tricarboxylic acid cycle	integral to membrane|mitochondrial respiratory chain	NAD binding|NAD(P)+ transhydrogenase (AB-specific) activity|NAD(P)+ transhydrogenase (B-specific) activity|NADP binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(6;2.58e-06)				NADH(DB00157)													---	---	---	---
FST	10468	broad.mit.edu	37	5	52779365	52779365	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52779365G>A	uc003jpd.2	+	3	336	c.309G>A	c.(307-309)GGG>GGA	p.G103G	FST_uc003jpc.2_Silent_p.G103G	NM_013409	NP_037541	P19883	FST_HUMAN	follistatin isoform FST344 precursor	103	Follistatin-like 1.|TB.				hemopoietic progenitor cell differentiation|negative regulation of activin receptor signaling pathway|negative regulation of follicle-stimulating hormone secretion|negative regulation of transcription from RNA polymerase II promoter|positive regulation of hair follicle development	extracellular region	activin binding|protein binding|signal transducer activity				0		Ovarian(174;1.78e-06)|Lung NSC(810;3.55e-06)|Breast(144;4.08e-05)																---	---	---	---
GZMA	3001	broad.mit.edu	37	5	54401360	54401360	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54401360G>T	uc003jpm.2	+	2	166	c.129G>T	c.(127-129)ATG>ATT	p.M43I		NM_006144	NP_006135	P12544	GRAA_HUMAN	granzyme A precursor	43	Peptidase S1.				cleavage of lamin|cytolysis|immune response|negative regulation of DNA binding|negative regulation of endodeoxyribonuclease activity|negative regulation of oxidoreductase activity|positive regulation of apoptosis	extracellular region|immunological synapse|nucleus	protein homodimerization activity|serine-type endopeptidase activity			ovary(2)|pancreas(1)|skin(1)	4		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.183)																---	---	---	---
DEPDC1B	55789	broad.mit.edu	37	5	59941361	59941361	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59941361T>C	uc003jsh.2	-	4	609	c.536A>G	c.(535-537)GAG>GGG	p.E179G	DEPDC1B_uc011cqm.1_Missense_Mutation_p.E179G|DEPDC1B_uc011cqn.1_Missense_Mutation_p.E152G	NM_018369	NP_060839	Q8WUY9	DEP1B_HUMAN	DEP domain containing 1B isoform 1	179					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(1)	1		Lung NSC(810;0.000214)|Prostate(74;0.0147)|Breast(144;0.0991)|Ovarian(174;0.17)																---	---	---	---
IPO11	51194	broad.mit.edu	37	5	61857070	61857070	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61857070G>A	uc003jtc.2	+	27	2758	c.2568G>A	c.(2566-2568)CTG>CTA	p.L856L	IPO11_uc011cqr.1_Silent_p.L896L|IPO11_uc003jtd.1_RNA|IPO11_uc010iwr.2_Silent_p.L121L	NM_016338	NP_057422	Q9UI26	IPO11_HUMAN	Ran binding protein 11 isoform 2	856	HEAT 14.					cytoplasm|nucleus	protein binding			lung(2)|skin(2)	4		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)														---	---	---	---
TRIM23	373	broad.mit.edu	37	5	64892366	64892366	+	Intron	SNP	A	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64892366A>T	uc003jty.2	-						TRIM23_uc003jtw.2_Intron|TRIM23_uc003jtx.2_Intron	NM_001656	NP_001647			ADP-ribosylation factor domain protein 1 isoform						interspecies interaction between organisms|small GTPase mediated signal transduction	Golgi membrane|lysosomal membrane	enzyme activator activity|GDP binding|GTP binding|GTPase activity|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|lung(1)	4		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Breast(144;0.0433)|Ovarian(174;0.0545)|Colorectal(97;0.234)		Lung(70;0.00473)														---	---	---	---
PIK3R1	5295	broad.mit.edu	37	5	67593304	67593304	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67593304C>T	uc003jva.2	+	16	2610	c.2050C>T	c.(2050-2052)CCC>TCC	p.P684S	PIK3R1_uc003jvb.2_Missense_Mutation_p.P684S|PIK3R1_uc003jvc.2_Missense_Mutation_p.P384S|PIK3R1_uc003jvd.2_Missense_Mutation_p.P414S|PIK3R1_uc003jve.2_Missense_Mutation_p.P363S	NM_181523	NP_852664	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1	684	SH2 2.				epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex	1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding	p.?(1)		endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1)	101		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoproterenol(DB01064)			Mis|F|O		gliobastoma|ovarian|colorectal					TCGA GBM(4;<1E-08)			---	---	---	---
MAP1B	4131	broad.mit.edu	37	5	71495745	71495745	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71495745C>A	uc003kbw.3	+	5	6804	c.6563C>A	c.(6562-6564)CCC>CAC	p.P2188H	MAP1B_uc010iyw.1_Missense_Mutation_p.P2205H|MAP1B_uc010iyx.1_Missense_Mutation_p.P2062H|MAP1B_uc010iyy.1_Missense_Mutation_p.P2062H	NM_005909	NP_005900	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	2188						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)														---	---	---	---
ZNF366	167465	broad.mit.edu	37	5	71756766	71756766	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71756766G>A	uc003kce.1	-	2	744	c.558C>T	c.(556-558)TTC>TTT	p.F186F		NM_152625	NP_689838	Q8N895	ZN366_HUMAN	zinc finger protein 366	186					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)|skin(1)	2		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)														---	---	---	---
F2R	2149	broad.mit.edu	37	5	76028461	76028461	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76028461G>A	uc003ken.3	+	2	676	c.411G>A	c.(409-411)GCG>GCA	p.A137A		NM_001992	NP_001983	P25116	PAR1_HUMAN	coagulation factor II receptor precursor	137	Cytoplasmic (Potential).				activation of caspase activity|anatomical structure morphogenesis|connective tissue replacement involved in inflammatory response wound healing|negative regulation of cell proliferation|platelet activation|positive regulation of blood coagulation|positive regulation of cell migration|positive regulation of collagen biosynthetic process|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of JAK-STAT cascade|positive regulation of MAPKKK cascade|positive regulation of release of sequestered calcium ion into cytosol|positive regulation of transcription, DNA-dependent|STAT protein import into nucleus|tyrosine phosphorylation of STAT protein	caveola|extracellular region|Golgi apparatus|integral to plasma membrane|platelet dense tubular network	receptor binding|thrombin receptor activity			ovary(3)	3		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Prostate(461;0.00955)|Ovarian(174;0.0129)		all cancers(79;4.43e-43)	Streptokinase(DB00086)													---	---	---	---
F2RL1	2150	broad.mit.edu	37	5	76129123	76129123	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76129123C>A	uc003keo.2	+	2	866	c.691C>A	c.(691-693)CCT>ACT	p.P231T		NM_005242	NP_005233	P55085	PAR2_HUMAN	coagulation factor II (thrombin) receptor-like 1	231	Extracellular (Potential).				blood coagulation|elevation of cytosolic calcium ion concentration|positive regulation of leukocyte chemotaxis|positive regulation of positive chemotaxis|regulation of blood coagulation	Golgi apparatus|integral to plasma membrane	receptor binding|thrombin receptor activity			central_nervous_system(1)	1		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;7.7e-51)|Epithelial(54;2.77e-45)|all cancers(79;3.47e-41)														---	---	---	---
PDE8B	8622	broad.mit.edu	37	5	76708046	76708046	+	Silent	SNP	C	T	T	rs140381860	byFrequency	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76708046C>T	uc003kfa.2	+	16	1743	c.1698C>T	c.(1696-1698)GCC>GCT	p.A566A	PDE8B_uc003kfb.2_Silent_p.A546A|PDE8B_uc003kfc.2_Silent_p.A511A|PDE8B_uc003kfd.2_Silent_p.A519A|PDE8B_uc003kfe.2_Silent_p.A469A	NM_003719	NP_003710	O95263	PDE8B_HUMAN	phosphodiesterase 8B isoform 1	566					cyclic nucleotide metabolic process|regulation of transcription, DNA-dependent	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|two-component response regulator activity				0		all_lung(232;0.00043)|Lung NSC(167;0.00114)|Ovarian(174;0.0107)|Prostate(461;0.0605)		OV - Ovarian serous cystadenocarcinoma(54;2.21e-49)|Epithelial(54;5.82e-43)|all cancers(79;4.06e-38)														---	---	---	---
WDR41	55255	broad.mit.edu	37	5	76736742	76736742	+	Missense_Mutation	SNP	G	A	A	rs17751013		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76736742G>A	uc003kff.1	-	9	1065	c.778C>T	c.(778-780)CGC>TGC	p.R260C	WDR41_uc011csy.1_Missense_Mutation_p.R202C|WDR41_uc011csz.1_Missense_Mutation_p.R205C|WDR41_uc011cta.1_RNA|WDR41_uc011ctb.1_RNA	NM_018268	NP_060738	Q9HAD4	WDR41_HUMAN	WD repeat domain 41	260											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)														---	---	---	---
SSBP2	23635	broad.mit.edu	37	5	80785136	80785136	+	Intron	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80785136A>G	uc003kho.2	-						SSBP2_uc010jar.2_Intron|SSBP2_uc003khn.2_Intron|SSBP2_uc003khp.2_Intron|SSBP2_uc011ctp.1_Intron|SSBP2_uc011ctq.1_Intron|SSBP2_uc011ctr.1_Intron	NM_012446	NP_036578			single-stranded DNA binding protein 2						regulation of transcription, DNA-dependent	cytoplasm|nucleus	single-stranded DNA binding		SSBP2/JAK2(4)	haematopoietic_and_lymphoid_tissue(4)|skin(1)	5		Lung NSC(167;0.00154)|all_lung(232;0.00179)|Ovarian(174;0.0338)		OV - Ovarian serous cystadenocarcinoma(54;1.07e-41)|Epithelial(54;2.79e-35)|all cancers(79;1.18e-29)														---	---	---	---
VCAN	1462	broad.mit.edu	37	5	82808018	82808018	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82808018A>G	uc003kii.3	+	6	1201	c.845A>G	c.(844-846)GAA>GGA	p.E282G	VCAN_uc003kij.3_Missense_Mutation_p.E282G|VCAN_uc010jau.2_Missense_Mutation_p.E282G|VCAN_uc003kik.3_Missense_Mutation_p.E282G|VCAN_uc003kih.3_Missense_Mutation_p.E282G	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1 precursor	282	Link 2.				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)														---	---	---	---
VCAN	1462	broad.mit.edu	37	5	82835516	82835516	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82835516A>C	uc003kii.3	+	8	7050	c.6694A>C	c.(6694-6696)AGT>CGT	p.S2232R	VCAN_uc003kij.3_Missense_Mutation_p.S1245R|VCAN_uc010jau.2_Intron|VCAN_uc003kik.3_Intron|VCAN_uc003kil.3_Missense_Mutation_p.S896R	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1 precursor	2232	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)														---	---	---	---
TTC37	9652	broad.mit.edu	37	5	94872785	94872785	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94872785G>T	uc003klb.2	-	9	874	c.604C>A	c.(604-606)CAA>AAA	p.Q202K	TTC37_uc010jbf.1_Missense_Mutation_p.Q154K	NM_014639	NP_055454	Q6PGP7	TTC37_HUMAN	tetratricopeptide repeat domain 37	202							binding			ovary(3)|pancreas(1)	4																		---	---	---	---
TTC37	9652	broad.mit.edu	37	5	94876500	94876500	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94876500C>T	uc003klb.2	-	8	707	c.437G>A	c.(436-438)CGG>CAG	p.R146Q	TTC37_uc010jbf.1_Missense_Mutation_p.R98Q	NM_014639	NP_055454	Q6PGP7	TTC37_HUMAN	tetratricopeptide repeat domain 37	146							binding			ovary(3)|pancreas(1)	4																		---	---	---	---
MAN2A1	4124	broad.mit.edu	37	5	109117301	109117301	+	Splice_Site	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109117301T>C	uc003kou.1	+	9	2540	c.1577_splice	c.e9+2	p.R526_splice		NM_002372	NP_002363			mannosidase, alpha, class 2A, member 1						mannose metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-mannosidase activity|carbohydrate binding|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)														---	---	---	---
TSLP	85480	broad.mit.edu	37	5	110407592	110407592	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110407592T>C	uc003kpb.2	+	1	203	c.4T>C	c.(4-6)TTC>CTC	p.F2L	TSLP_uc003kpa.2_Intron|TSLP_uc010jbt.1_5'Flank	NM_033035	NP_149024	Q969D9	TSLP_HUMAN	thymic stromal lymphopoietin isoform 1	2				MFPFALLYVLS -> MKCLGQSKKEE (in Ref. 3; AAH40592).		extracellular space	cytokine activity				0		all_cancers(142;2.72e-05)|all_epithelial(76;4.39e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0417)|Ovarian(225;0.0443)|Colorectal(57;0.0464)|all_lung(232;0.0507)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.24e-08)|Epithelial(69;1.54e-07)|all cancers(49;1.73e-05)|COAD - Colon adenocarcinoma(37;0.109)														---	---	---	---
SEMA6A	57556	broad.mit.edu	37	5	115783245	115783245	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115783245C>T	uc010jck.2	-	19	2866	c.2157G>A	c.(2155-2157)CCG>CCA	p.P719P	SEMA6A_uc003krx.3_Silent_p.P736P|SEMA6A_uc011cwe.1_Silent_p.P98P|SEMA6A_uc003krv.3_Silent_p.P146P|SEMA6A_uc003krw.3_Silent_p.P196P|SEMA6A_uc010jcj.2_Silent_p.P263P	NM_020796	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and	719	Cytoplasmic (Potential).				apoptosis|axon guidance|cell surface receptor linked signaling pathway|cytoskeleton organization|organ morphogenesis	axon|integral to membrane|plasma membrane	receptor activity			ovary(2)	2		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)														---	---	---	---
TNFAIP8	25816	broad.mit.edu	37	5	118728939	118728939	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118728939C>T	uc003ksh.2	+	3	1148	c.460C>T	c.(460-462)CGG>TGG	p.R154W	TNFAIP8_uc003ksf.1_3'UTR|TNFAIP8_uc003ksg.2_Missense_Mutation_p.R144W|TNFAIP8_uc011cwf.1_Missense_Mutation_p.R148W|TNFAIP8_uc003ksi.2_Missense_Mutation_p.R154W	NM_014350	NP_055165	O95379	TFIP8_HUMAN	tumor necrosis factor, alpha-induced protein 8	154					anti-apoptosis|apoptosis|negative regulation of anti-apoptosis	cytoplasm	caspase inhibitor activity|protein binding			ovary(1)	1		all_cancers(142;0.0317)|Prostate(80;0.111)|Breast(839;0.231)		Epithelial(69;4.63e-83)|OV - Ovarian serous cystadenocarcinoma(64;1.39e-82)|all cancers(49;4.88e-75)|GBM - Glioblastoma multiforme(465;0.00338)|BRCA - Breast invasive adenocarcinoma(61;0.0148)|COAD - Colon adenocarcinoma(49;0.0829)														---	---	---	---
LOX	4015	broad.mit.edu	37	5	121411121	121411121	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121411121A>C	uc003ksu.2	-	3	1231	c.856T>G	c.(856-858)TGG>GGG	p.W286G	LOX_uc010jcp.2_5'Flank|LOX_uc010jcq.2_5'UTR|LOX_uc011cwk.1_Missense_Mutation_p.W56G|LOX_uc010jcr.2_5'UTR	NM_002317	NP_002308	P28300	LYOX_HUMAN	lysyl oxidase preproprotein	286	Lysyl-oxidase like.				protein modification process	extracellular space	copper ion binding|protein-lysine 6-oxidase activity			lung(1)	1		all_cancers(142;0.0124)|Prostate(80;0.0322)|Ovarian(225;0.0814)|Breast(839;0.143)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;2.14e-11)|OV - Ovarian serous cystadenocarcinoma(64;7.87e-10)|all cancers(49;2.49e-09)|COAD - Colon adenocarcinoma(49;0.02)														---	---	---	---
PPIC	5480	broad.mit.edu	37	5	122359691	122359691	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122359691A>G	uc003kth.2	-	5	623	c.518T>C	c.(517-519)GTG>GCG	p.V173A		NM_000943	NP_000934	P45877	PPIC_HUMAN	peptidylprolyl isomerase C	173	PPIase cyclophilin-type.				protein folding|signal transduction	cytoplasm	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity|unfolded protein binding			ovary(1)	1		all_cancers(142;0.0168)|Prostate(80;0.0322)|Lung NSC(810;0.102)|all_lung(232;0.163)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	OV - Ovarian serous cystadenocarcinoma(64;0.000331)|Epithelial(69;0.000553)|all cancers(49;0.00505)	L-Proline(DB00172)													---	---	---	---
PRRC1	133619	broad.mit.edu	37	5	126865993	126865993	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126865993C>T	uc003kuk.2	+	5	842	c.662C>T	c.(661-663)GCT>GTT	p.A221V	PRRC1_uc003kuj.3_Missense_Mutation_p.A221V	NM_130809	NP_570721	Q96M27	PRRC1_HUMAN	proline-rich coiled-coil 1	221						Golgi apparatus					0		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0851)|Epithelial(69;0.113)														---	---	---	---
FBN2	2201	broad.mit.edu	37	5	127595450	127595450	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127595450G>A	uc003kuu.2	-	65	8875	c.8436C>T	c.(8434-8436)CTC>CTT	p.L2812L		NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor	2812					bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)														---	---	---	---
FBN2	2201	broad.mit.edu	37	5	127644961	127644961	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127644961T>C	uc003kuu.2	-	41	5770	c.5331A>G	c.(5329-5331)GAA>GAG	p.E1777E		NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor	1777	TB 7.				bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)														---	---	---	---
SEPT8	23176	broad.mit.edu	37	5	132101186	132101186	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132101186G>A	uc003kxr.2	-	2	304	c.66C>T	c.(64-66)GGC>GGT	p.G22G	SEPT8_uc003kxs.1_Silent_p.G22G|SEPT8_uc003kxu.2_Silent_p.G22G|SEPT8_uc011cxi.1_Silent_p.G22G|SEPT8_uc003kxv.2_Silent_p.G22G|SEPT8_uc003kxt.2_5'UTR	NM_001098811	NP_001092281	Q92599	SEPT8_HUMAN	septin 8 isoform a	22					cell cycle	septin complex	GTP binding|protein binding			ovary(2)	2		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
VDAC1	7416	broad.mit.edu	37	5	133309532	133309532	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133309532A>G	uc003kyp.1	-	8	809	c.710T>C	c.(709-711)GTG>GCG	p.V237A	VDAC1_uc003kyq.1_Missense_Mutation_p.V237A|VDAC1_uc003kyr.1_Missense_Mutation_p.V237A	NM_003374	NP_003365	P21796	VDAC1_HUMAN	voltage-dependent anion channel 1	237	Beta stranded.				apoptosis|interspecies interaction between organisms	mitochondrial nucleoid|mitochondrial outer membrane|plasma membrane|pore complex	porin activity|protein binding|voltage-gated anion channel activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00806)|Kidney(363;0.02)		Dihydroxyaluminium(DB01375)													---	---	---	---
PHF15	23338	broad.mit.edu	37	5	133887788	133887788	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133887788A>G	uc003kzo.1	+	4	379	c.200A>G	c.(199-201)TAC>TGC	p.Y67C	PHF15_uc011cxt.1_Missense_Mutation_p.Y67C|PHF15_uc003kzk.2_Missense_Mutation_p.Y83C|PHF15_uc003kzl.2_Missense_Mutation_p.Y67C|PHF15_uc003kzm.2_Missense_Mutation_p.Y67C|PHF15_uc003kzn.2_Missense_Mutation_p.Y67C	NM_015288	NP_056103	Q9NQC1	JADE2_HUMAN	PHD finger protein 15	67					histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
TGFBI	7045	broad.mit.edu	37	5	135388774	135388774	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135388774C>T	uc003lbf.3	+	8	1253	c.1092C>T	c.(1090-1092)ATC>ATT	p.I364I	TGFBI_uc003lbg.3_Silent_p.I97I|TGFBI_uc003lbh.3_Silent_p.I190I|TGFBI_uc011cyb.1_Silent_p.I190I|TGFBI_uc010jed.2_Silent_p.I97I	NM_000358	NP_000349	Q15582	BGH3_HUMAN	transforming growth factor, beta-induced, 68kDa	364	FAS1 2.				angiogenesis|cell adhesion|cell proliferation|negative regulation of cell adhesion|response to stimulus|visual perception	extracellular space|proteinaceous extracellular matrix	integrin binding			breast(3)|ovary(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
PKD2L2	27039	broad.mit.edu	37	5	137271531	137271531	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137271531G>T	uc003lby.2	+	13	1773	c.1717G>T	c.(1717-1719)GAG>TAG	p.E573*	PKD2L2_uc003lbw.1_Nonsense_Mutation_p.E573*|PKD2L2_uc003lbx.2_Nonsense_Mutation_p.E472*|PKD2L2_uc011cyi.1_Nonsense_Mutation_p.E181*	NM_014386	NP_055201	Q9NZM6	PK2L2_HUMAN	polycystic kidney disease 2-like 2	573	Cytoplasmic (Potential).|Potential.					integral to membrane	calcium ion binding|ion channel activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)															---	---	---	---
HSPA9	3313	broad.mit.edu	37	5	137892463	137892463	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137892463C>A	uc003ldf.2	-	15	1929	c.1821G>T	c.(1819-1821)GAG>GAT	p.E607D	HSPA9_uc003lde.2_Missense_Mutation_p.E24D	NM_004134	NP_004125	P38646	GRP75_HUMAN	heat shock 70kDa protein 9 precursor	607					anti-apoptosis|protein folding	cell surface|mitochondrial nucleoid	ATP binding|unfolded protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)															---	---	---	---
SLC23A1	9963	broad.mit.edu	37	5	138713715	138713715	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138713715C>T	uc003leh.2	-	12	1499	c.1402G>A	c.(1402-1404)GGG>AGG	p.G468R	SLC23A1_uc003leg.2_Missense_Mutation_p.G472R	NM_005847	NP_005838	Q9UHI7	S23A1_HUMAN	solute carrier family 23 (nucleobase	468	Helical; (Potential).				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)													---	---	---	---
APBB3	10307	broad.mit.edu	37	5	139943451	139943451	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139943451A>G	uc003lgd.1	-	2	458	c.99T>C	c.(97-99)CCT>CCC	p.P33P	APBB3_uc003lgb.1_5'Flank|APBB3_uc003lgc.1_5'UTR|APBB3_uc003lge.1_Silent_p.P33P|APBB3_uc003lgf.1_RNA|APBB3_uc010jfp.1_RNA|APBB3_uc011czi.1_5'UTR|APBB3_uc010jfq.1_5'Flank|APBB3_uc010jfr.1_Silent_p.P33P|SLC35A4_uc003lgg.1_5'Flank|SLC35A4_uc003lgh.1_5'Flank	NM_133172	NP_573418	O95704	APBB3_HUMAN	amyloid beta precursor protein-binding, family	33	WW.					actin cytoskeleton|cytoplasm				ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
CD14	929	broad.mit.edu	37	5	140011549	140011549	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140011549G>A	uc003lgi.1	-	2	1374	c.1020C>T	c.(1018-1020)CAC>CAT	p.H340H	CD14_uc003lgj.1_Silent_p.H340H	NM_000591	NP_000582	P08571	CD14_HUMAN	CD14 antigen precursor	340	LRR 11.				apoptosis|cellular response to lipopolysaccharide|cellular response to lipoteichoic acid|inflammatory response|innate immune response|phagocytosis|positive regulation of tumor necrosis factor production|Toll signaling pathway	anchored to membrane|plasma membrane	lipopolysaccharide binding|lipoteichoic acid binding|opsonin receptor activity|peptidoglycan receptor activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
TMCO6	55374	broad.mit.edu	37	5	140023376	140023376	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140023376C>T	uc003lgl.2	+	9	1031	c.930C>T	c.(928-930)CCC>CCT	p.P310P	TMCO6_uc003lgm.2_Silent_p.P316P|TMCO6_uc010jft.2_Silent_p.P70P|TMCO6_uc003lgn.2_Silent_p.P201P|TMCO6_uc003lgo.2_Silent_p.P70P	NM_018502	NP_060972	Q96DC7	TMCO6_HUMAN	transmembrane and coiled-coil domains 6	310					protein import into nucleus	cytoplasm|nuclear pore	binding|protein transporter activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA2	56146	broad.mit.edu	37	5	140174643	140174643	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140174643C>T	uc003lhd.2	+	1	200	c.94C>T	c.(94-96)CGC>TGC	p.R32C	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhc.1_Missense_Mutation_p.R32C|PCDHA2_uc011czy.1_Missense_Mutation_p.R32C	NM_018905	NP_061728	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2 isoform 1 precursor	32	Extracellular (Potential).|Cadherin 1.				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)															---	---	---	---
PCDHA5	56143	broad.mit.edu	37	5	140202821	140202821	+	Silent	SNP	C	A	A	rs80008076	byFrequency	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140202821C>A	uc003lhl.2	+	1	1461	c.1461C>A	c.(1459-1461)GCC>GCA	p.A487A	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_Silent_p.A487A|PCDHA5_uc003lhj.1_Silent_p.A487A	NM_018908	NP_061731	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5 isoform 1 precursor	487	Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(1)|breast(1)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA9	9752	broad.mit.edu	37	5	140228225	140228225	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140228225G>A	uc003lhu.2	+	1	869	c.145G>A	c.(145-147)GCG>ACG	p.A49T	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lht.1_Missense_Mutation_p.A49T	NM_031857	NP_114063	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9 isoform 1 precursor	49	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding			large_intestine(2)|ovary(2)|skin(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA9	9752	broad.mit.edu	37	5	140229614	140229614	+	Missense_Mutation	SNP	G	A	A	rs143144725	byFrequency	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140229614G>A	uc003lhu.2	+	1	2258	c.1534G>A	c.(1534-1536)GCG>ACG	p.A512T	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lht.1_Missense_Mutation_p.A512T	NM_031857	NP_114063	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9 isoform 1 precursor	512	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding			large_intestine(2)|ovary(2)|skin(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHB2	56133	broad.mit.edu	37	5	140475461	140475461	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140475461C>A	uc003lil.2	+	1	1225	c.1087C>A	c.(1087-1089)CAG>AAG	p.Q363K	PCDHB2_uc003lim.1_Missense_Mutation_p.Q24K	NM_018936	NP_061759	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2 precursor	363	Extracellular (Potential).|Cadherin 4.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			ovary(3)|upper_aerodigestive_tract(2)|pancreas(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB10	56126	broad.mit.edu	37	5	140573540	140573540	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140573540G>A	uc003lix.2	+	1	1589	c.1415G>A	c.(1414-1416)AGC>AAC	p.S472N		NM_018930	NP_061753	Q9UN67	PCDBA_HUMAN	protocadherin beta 10 precursor	472	Cadherin 5.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB10	56126	broad.mit.edu	37	5	140573784	140573784	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140573784C>T	uc003lix.2	+	1	1833	c.1659C>T	c.(1657-1659)GAC>GAT	p.D553D		NM_018930	NP_061753	Q9UN67	PCDBA_HUMAN	protocadherin beta 10 precursor	553	Cadherin 5.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHGA3	56112	broad.mit.edu	37	5	140725041	140725041	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140725041A>G	uc003ljm.1	+	1	1441	c.1441A>G	c.(1441-1443)AGC>GGC	p.S481G	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_Missense_Mutation_p.S241G|PCDHGA3_uc011dap.1_Missense_Mutation_p.S481G	NM_018916	NP_061739	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3 isoform 1	481	Extracellular (Potential).|Cadherin 5.				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)															---	---	---	---
PCDHGA3	56112	broad.mit.edu	37	5	140725097	140725097	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140725097G>A	uc003ljm.1	+	1	1497	c.1497G>A	c.(1495-1497)GCG>GCA	p.A499A	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_Silent_p.A259A|PCDHGA3_uc011dap.1_Silent_p.A499A	NM_018916	NP_061739	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3 isoform 1	499	Extracellular (Potential).|Cadherin 5.				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)															---	---	---	---
PCDHGB3	56102	broad.mit.edu	37	5	140751710	140751710	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140751710G>T	uc003ljw.1	+	1	1749	c.1749G>T	c.(1747-1749)GAG>GAT	p.E583D	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|PCDHGA6_uc003ljy.1_5'Flank|PCDHGB3_uc011dat.1_Missense_Mutation_p.E583D|PCDHGA6_uc011dau.1_5'Flank	NM_018924	NP_061747	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3 isoform 1	583	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)															---	---	---	---
PCDHGA7	56108	broad.mit.edu	37	5	140764553	140764553	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140764553C>T	uc003lka.1	+	1	2087	c.2087C>T	c.(2086-2088)GCG>GTG	p.A696V	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|PCDHGB4_uc003lkc.1_5'Flank|PCDHGA7_uc003ljz.1_Missense_Mutation_p.A696V|PCDHGB4_uc011dav.1_5'Flank	NM_018920	NP_061743	Q9Y5G6	PCDG7_HUMAN	protocadherin gamma subfamily A, 7 isoform 1	696	Helical; (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGA11	56105	broad.mit.edu	37	5	140801090	140801090	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140801090C>T	uc003lkq.1	+	1	554	c.296C>T	c.(295-297)ACG>ATG	p.T99M	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.T99M|PCDHGA11_uc003lkp.1_Missense_Mutation_p.T99M	NM_018914	NP_061737	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11 isoform 1	99	Extracellular (Potential).|Cadherin 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)															---	---	---	---
DPYSL3	1809	broad.mit.edu	37	5	146780279	146780279	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146780279C>T	uc003lon.1	-	10	1196	c.1086G>A	c.(1084-1086)ATG>ATA	p.M362I	DPYSL3_uc003loo.2_Missense_Mutation_p.M476I	NM_001387	NP_001378	Q14195	DPYL3_HUMAN	dihydropyrimidinase-like 3	362					axon guidance|pyrimidine base catabolic process|signal transduction	cytosol|growth cone	dihydropyrimidinase activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCYOX1L	78991	broad.mit.edu	37	5	148745642	148745642	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148745642G>A	uc003lqk.2	+	4	670	c.608G>A	c.(607-609)CGC>CAC	p.R203H	PCYOX1L_uc003lql.2_Missense_Mutation_p.R186H|PCYOX1L_uc010jgz.2_Intron|PCYOX1L_uc003lqm.2_Missense_Mutation_p.R85H|PCYOX1L_uc003lqn.2_Missense_Mutation_p.R113H	NM_024028	NP_076933	Q8NBM8	PCYXL_HUMAN	prenylcysteine oxidase 1 like precursor	203					prenylcysteine catabolic process	extracellular region	oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
TIGD6	81789	broad.mit.edu	37	5	149375786	149375786	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149375786A>G	uc003lri.2	-	2	888	c.126T>C	c.(124-126)TCT>TCC	p.S42S	TIGD6_uc003lrj.2_Silent_p.S42S	NM_030953	NP_112215	Q17RP2	TIGD6_HUMAN	hypothetical protein LOC81789	42	H-T-H motif (By similarity).|HTH psq-type.				regulation of transcription, DNA-dependent	chromosome, centromeric region|nucleus	DNA binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)															---	---	---	---
PDGFRB	5159	broad.mit.edu	37	5	149505041	149505041	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149505041T>C	uc003lro.2	-	12	2243	c.1774A>G	c.(1774-1776)ACG>GCG	p.T592A	PDGFRB_uc010jhd.2_Missense_Mutation_p.T431A	NM_002609	NP_002600	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor beta	592	Cytoplasmic (Potential).				aorta morphogenesis|cardiac myofibril assembly|hemopoiesis|metanephric glomerular capillary formation|metanephric glomerular mesangial cell proliferation involved in metanephros development|peptidyl-tyrosine phosphorylation|positive regulation of calcium ion import|positive regulation of chemotaxis|positive regulation of DNA biosynthetic process|positive regulation of ERK1 and ERK2 cascade|positive regulation of MAP kinase activity|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway|positive regulation of mitosis|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of reactive oxygen species metabolic process|positive regulation of smooth muscle cell migration|positive regulation of smooth muscle cell proliferation|protein autophosphorylation|regulation of actin cytoskeleton organization|retina vasculature development in camera-type eye|smooth muscle cell chemotaxis	apical plasma membrane|cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet activating factor receptor activity|platelet-derived growth factor beta-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|vascular endothelial growth factor receptor activity			central_nervous_system(4)|lung(4)|breast(3)|stomach(2)|prostate(2)|large_intestine(1)|ovary(1)	17		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Becaplermin(DB00102)|Dasatinib(DB01254)|Imatinib(DB00619)|Sorafenib(DB00398)|Sunitinib(DB01268)			T	ETV6|TRIP11|HIP1|RAB5EP|H4|NIN|HCMOGT-1|PDE4DIP	MPD|AML|CMML|CML								---	---	---	---
FAT2	2196	broad.mit.edu	37	5	150885266	150885266	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150885266G>A	uc003lue.3	-	23	12923	c.12910C>T	c.(12910-12912)CGA>TGA	p.R4304*	GM2A_uc011dcs.1_Intron|FAT2_uc003lud.3_Nonsense_Mutation_p.R911*	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	4304	Cytoplasmic (Potential).				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)|upper_aerodigestive_tract(1)|skin(1)	6		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
IL12B	3593	broad.mit.edu	37	5	158747463	158747463	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158747463T>C	uc003lxr.1	-	5	590	c.548A>G	c.(547-549)GAC>GGC	p.D183G		NM_002187	NP_002178	P29460	IL12B_HUMAN	interleukin 12B precursor	183					cell cycle arrest|cell migration|defense response to Gram-negative bacterium|interferon-gamma biosynthetic process|natural killer cell activation|negative regulation of interleukin-10 production|negative regulation of interleukin-17 production|negative regulation of smooth muscle cell proliferation|positive regulation of activated T cell proliferation|positive regulation of activation of JAK2 kinase activity|positive regulation of cell adhesion|positive regulation of defense response to virus by host|positive regulation of granulocyte macrophage colony-stimulating factor production|positive regulation of interferon-gamma biosynthetic process|positive regulation of interferon-gamma production|positive regulation of interleukin-10 production|positive regulation of interleukin-12 production|positive regulation of interleukin-17 production|positive regulation of memory T cell differentiation|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target|positive regulation of natural killer cell proliferation|positive regulation of NF-kappaB import into nucleus|positive regulation of NK T cell activation|positive regulation of NK T cell proliferation|positive regulation of osteoclast differentiation|positive regulation of smooth muscle cell apoptosis|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|positive regulation of tumor necrosis factor production|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat4 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|regulation of tyrosine phosphorylation of Stat1 protein|response to UV-B|sexual reproduction|T-helper 1 type immune response|T-helper cell differentiation	interleukin-12 complex|interleukin-23 complex|membrane	cytokine activity|cytokine receptor activity|interleukin-12 receptor binding|protein heterodimerization activity				0	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
STC2	8614	broad.mit.edu	37	5	172750298	172750298	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172750298C>T	uc003mco.1	-	3	1740	c.430G>A	c.(430-432)GAC>AAC	p.D144N	STC2_uc003mcn.1_Missense_Mutation_p.D59N	NM_003714	NP_003705	O76061	STC2_HUMAN	stanniocalcin 2 precursor	144					cell surface receptor linked signaling pathway|cell-cell signaling	extracellular region	hormone activity			skin(2)|ovary(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|Ovarian(839;0.223)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)															---	---	---	---
SLC34A1	6569	broad.mit.edu	37	5	176825048	176825048	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176825048C>A	uc003mgk.3	+	13	1782	c.1681C>A	c.(1681-1683)CTG>ATG	p.L561M		NM_003052	NP_003043	Q06495	NPT2A_HUMAN	solute carrier family 34 (sodium phosphate),	561	Helical; Name=M8; (Potential).				phosphate ion homeostasis|response to cadmium ion|response to lead ion|response to mercury ion|sodium ion transport	brush border membrane|integral to plasma membrane	protein binding|sodium-dependent phosphate transmembrane transporter activity|symporter activity			ovary(1)	1	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)															---	---	---	---
DDX41	51428	broad.mit.edu	37	5	176939353	176939353	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176939353T>C	uc003mho.2	-	15	1612	c.1591A>G	c.(1591-1593)ATC>GTC	p.I531V	DOK3_uc003mhi.3_5'Flank|DOK3_uc003mhj.3_5'Flank|DOK3_uc003mhk.2_5'Flank|DOK3_uc003mhl.2_5'Flank|DDX41_uc003mhm.2_Missense_Mutation_p.I311V|DDX41_uc003mhn.2_Missense_Mutation_p.I400V|DDX41_uc003mhp.2_Missense_Mutation_p.I400V	NM_016222	NP_057306	Q9UJV9	DDX41_HUMAN	DEAD-box protein abstrakt	531	Helicase C-terminal.				apoptosis|multicellular organismal development	catalytic step 2 spliceosome	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding|zinc ion binding				0	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)|Epithelial(233;0.191)															---	---	---	---
RMND5B	64777	broad.mit.edu	37	5	177569904	177569904	+	Missense_Mutation	SNP	C	T	T	rs142045405		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177569904C>T	uc003mim.2	+	5	517	c.337C>T	c.(337-339)CGG>TGG	p.R113W	RMND5B_uc003min.2_Missense_Mutation_p.R113W|RMND5B_uc003mio.2_Missense_Mutation_p.R100W|RMND5B_uc003mip.2_Missense_Mutation_p.R113W|RMND5B_uc011dgf.1_Missense_Mutation_p.R154W|RMND5B_uc003miq.2_Missense_Mutation_p.R53W	NM_022762	NP_073599	Q96G75	RMD5B_HUMAN	required for meiotic nuclear division 5 homolog	113										ovary(1)|skin(1)	2	all_cancers(89;0.00294)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
ZNF354B	117608	broad.mit.edu	37	5	178310410	178310410	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178310410C>T	uc003mjl.2	+	5	1183	c.957C>T	c.(955-957)ATC>ATT	p.I319I	ZNF354B_uc003mjm.2_Silent_p.I319I	NM_058230	NP_478137	Q96LW1	Z354B_HUMAN	zinc finger protein 354B	319	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
FAM50B	26240	broad.mit.edu	37	6	3850082	3850082	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3850082C>A	uc003mvu.2	+	2	149	c.37C>A	c.(37-39)CGT>AGT	p.R13S		NM_012135	NP_036267	Q9Y247	FA50B_HUMAN	family with sequence similarity 50, member B	13						nucleus				pancreas(1)	1	Ovarian(93;0.0925)	all_hematologic(90;0.108)																---	---	---	---
FARS2	10667	broad.mit.edu	37	6	5771613	5771613	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5771613C>T	uc010jnv.1	+	7	1643	c.1307C>T	c.(1306-1308)GCC>GTC	p.A436V	FARS2_uc003mwr.2_Missense_Mutation_p.A436V	NM_006567	NP_006558	O95363	SYFM_HUMAN	phenylalanyl-tRNA synthetase 2 precursor	436	FDX-ACB.				phenylalanyl-tRNA aminoacylation|tRNA processing	mitochondrial matrix|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding				0	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)													---	---	---	---
RREB1	6239	broad.mit.edu	37	6	7230312	7230312	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7230312C>T	uc003mxc.2	+	10	2370	c.1980C>T	c.(1978-1980)GCC>GCT	p.A660A	RREB1_uc003mxb.2_Silent_p.A660A|RREB1_uc010jnx.2_Silent_p.A660A	NM_001003698	NP_001003698	Q92766	RREB1_HUMAN	ras responsive element binding protein 1 isoform	660	C2H2-type 7.				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	7247443	7247443	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7247443G>A	uc003mxc.2	+	11	4985	c.4595G>A	c.(4594-4596)CGC>CAC	p.R1532H	RREB1_uc003mxb.2_Missense_Mutation_p.R1587H|RREB1_uc010jnx.2_Intron	NM_001003698	NP_001003698	Q92766	RREB1_HUMAN	ras responsive element binding protein 1 isoform	1532	C2H2-type 14.				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)																---	---	---	---
MYLIP	29116	broad.mit.edu	37	6	16129621	16129621	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16129621G>A	uc003nbq.2	+	1	305	c.68G>A	c.(67-69)GGC>GAC	p.G23D	MYLIP_uc003nbr.2_5'UTR	NM_013262	NP_037394	Q8WY64	MYLIP_HUMAN	myosin regulatory light chain interacting	23	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)															---	---	---	---
FAM8A1	51439	broad.mit.edu	37	6	17606227	17606227	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17606227A>G	uc003ncc.2	+	4	1203	c.1080A>G	c.(1078-1080)TCA>TCG	p.S360S		NM_016255	NP_057339	Q9UBU6	FA8A1_HUMAN	family with sequence similarity 8, member A1	360	RDD.					integral to membrane					0	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.143)	all cancers(50;0.176)|Epithelial(50;0.204)															---	---	---	---
SCAND3	114821	broad.mit.edu	37	6	28542729	28542729	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28542729T>C	uc003nlo.2	-	3	2371	c.1753A>G	c.(1753-1755)ACT>GCT	p.T585A		NM_052923	NP_443155	Q6R2W3	SCND3_HUMAN	SCAN domain containing 3	585					DNA integration|viral reproduction	nucleus	DNA binding|protein dimerization activity|sequence-specific DNA binding transcription factor activity			ovary(1)	1																		---	---	---	---
OR14J1	442191	broad.mit.edu	37	6	29275424	29275424	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29275424A>G	uc011dln.1	+	1	958	c.958A>G	c.(958-960)AAA>GAA	p.K320E		NM_030946	NP_112208	Q9UGF5	O14J1_HUMAN	olfactory receptor, family 5, subfamily U member	320	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1																		---	---	---	---
OR12D2	26529	broad.mit.edu	37	6	29364516	29364516	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29364516G>A	uc003nmf.3	+	1	101	c.40G>A	c.(40-42)GGA>AGA	p.G14R		NM_013936	NP_039224	P58182	O12D2_HUMAN	olfactory receptor, family 12, subfamily D,	14	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1																		---	---	---	---
OR12D2	26529	broad.mit.edu	37	6	29365078	29365078	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29365078C>T	uc003nmf.3	+	1	663	c.602C>T	c.(601-603)ACG>ATG	p.T201M		NM_013936	NP_039224	P58182	O12D2_HUMAN	olfactory receptor, family 12, subfamily D,	201	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1																		---	---	---	---
OR2H2	7932	broad.mit.edu	37	6	29556527	29556527	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29556527G>A	uc003nmr.1	+	1	845	c.806G>A	c.(805-807)GGC>GAC	p.G269D	GABBR1_uc003nmp.3_Intron	NM_007160	NP_009091	O95918	OR2H2_HUMAN	olfactory receptor, family 2, subfamily H,	269	Extracellular (Potential).				defense response|mating|sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0																		---	---	---	---
HLA-C	3107	broad.mit.edu	37	6	31239616	31239616	+	Missense_Mutation	SNP	C	A	A	rs1050445		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31239616C>A	uc003nsy.2	-	2	110	c.103G>T	c.(103-105)GCC>TCC	p.A35S	HLA-C_uc011dnj.1_Missense_Mutation_p.A7S|HLA-C_uc003nsx.2_5'UTR|HLA-C_uc003nsz.2_Missense_Mutation_p.A35S|HLA-C_uc010jsl.2_Missense_Mutation_p.A35S|HLA-C_uc003nta.2_Missense_Mutation_p.A35S|HLA-C_uc003ntb.2_Intron|HLA-C_uc003ntc.1_Intron|HLA-B_uc010jsm.1_Intron|HLA-B_uc011dnk.1_Intron|HLA-C_uc011dnl.1_5'UTR|HLA-B_uc003ntf.2_Intron	NM_002117	NP_002108	Q9TNN7	1C05_HUMAN	major histocompatibility complex, class I, C	35	Extracellular (Potential).|Alpha-1.				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 membrane|MHC class I protein complex					0																		---	---	---	---
BAT2	7916	broad.mit.edu	37	6	31600179	31600179	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31600179G>A	uc003nvb.3	+	16	3978	c.3729G>A	c.(3727-3729)AGG>AGA	p.R1243R	BAT2_uc011dnv.1_Intron|BAT2_uc003nvc.3_Silent_p.R1243R	NM_080686	NP_542417	P48634	PRC2A_HUMAN	HLA-B associated transcript-2	1243	Poly-Arg.|4 X 57 AA type A repeats.					cytoplasm|nucleus	protein binding				0																		---	---	---	---
MSH5	4439	broad.mit.edu	37	6	31727670	31727670	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31727670C>T	uc003nwv.1	+	18	1682	c.1603C>T	c.(1603-1605)CTT>TTT	p.L535F	MSH5_uc003nwt.1_Missense_Mutation_p.L552F|MSH5_uc003nwu.1_Missense_Mutation_p.L535F|MSH5_uc003nww.1_Missense_Mutation_p.L535F|MSH5_uc003nwx.1_Missense_Mutation_p.L552F|MSH5_uc011dof.1_Missense_Mutation_p.L234F|MSH5_uc003nwy.1_Missense_Mutation_p.L209F|MSH5_uc003nwz.3_RNA	NM_172166	NP_751898	O43196	MSH5_HUMAN	mutS homolog 5 isoform c	535					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					---	---	---	---
SKIV2L	6499	broad.mit.edu	37	6	31931748	31931748	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31931748T>C	uc003nyn.1	+	16	2095	c.1706T>C	c.(1705-1707)GTG>GCG	p.V569A	SKIV2L_uc011dou.1_Missense_Mutation_p.V411A|SKIV2L_uc011dov.1_Missense_Mutation_p.V376A	NM_006929	NP_008860	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like homolog	569						nucleus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(1)|large_intestine(1)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
ITPR3	3710	broad.mit.edu	37	6	33657855	33657855	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33657855T>C	uc011drk.1	+	51	7131	c.6912T>C	c.(6910-6912)CGT>CGC	p.R2304R	ITPR3_uc003oey.2_Silent_p.R391R	NM_002224	NP_002215	Q14573	ITPR3_HUMAN	inositol 1,4,5-triphosphate receptor, type 3	2304	Extracellular (Potential).				activation of phospholipase C activity|calcium ion transport into cytosol|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|protein heterooligomerization|protein homooligomerization|regulation of insulin secretion|response to calcium ion	apical part of cell|brush border|endoplasmic reticulum membrane|integral to plasma membrane|myelin sheath|neuronal cell body|nuclear outer membrane|platelet dense tubular network membrane	inositol 1,3,4,5 tetrakisphosphate binding|inositol 1,4,5 trisphosphate binding|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|inositol hexakisphosphate binding|intracellular ligand-gated calcium channel activity|protein binding			ovary(6)|lung(5)|central_nervous_system(5)|breast(2)|kidney(1)	19																		---	---	---	---
PPARD	5467	broad.mit.edu	37	6	35389634	35389634	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35389634A>G	uc003okm.2	+	5	632	c.323A>G	c.(322-324)TAC>TGC	p.Y108C	PPARD_uc003okl.2_Missense_Mutation_p.Y108C|PPARD_uc003okn.2_Missense_Mutation_p.Y108C|PPARD_uc011dtb.1_Missense_Mutation_p.Y69C|PPARD_uc011dtc.1_Intron|PPARD_uc010jvv.1_RNA	NM_006238	NP_006229	Q03181	PPARD_HUMAN	peroxisome proliferative activated receptor,	108	Nuclear receptor.				apoptosis|axon ensheathment|cholesterol metabolic process|decidualization|embryo implantation|fatty acid beta-oxidation|fatty acid transport|generation of precursor metabolites and energy|glucose metabolic process|glucose transport|negative regulation of transcription from RNA polymerase II promoter|positive regulation of fat cell differentiation|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	drug binding|linoleic acid binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)	1					Icosapent(DB00159)|Sulindac(DB00605)|Treprostinil(DB00374)													---	---	---	---
BRPF3	27154	broad.mit.edu	37	6	36198270	36198270	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36198270C>A	uc003olv.3	+	13	3726	c.3502C>A	c.(3502-3504)CTG>ATG	p.L1168M	BRPF3_uc010jwb.2_Missense_Mutation_p.L898M|BRPF3_uc011dtj.1_RNA|BRPF3_uc010jwc.2_RNA|BRPF3_uc011dtk.1_Missense_Mutation_p.L834M|BRPF3_uc010jwd.2_Missense_Mutation_p.L70M	NM_015695	NP_056510	Q9ULD4	BRPF3_HUMAN	bromodomain and PHD finger containing, 3	1168					histone H3 acetylation|platelet activation|platelet degranulation	cytosol|extracellular region|MOZ/MORF histone acetyltransferase complex	protein binding|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
TREM2	54209	broad.mit.edu	37	6	41129205	41129205	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41129205C>T	uc003opy.2	-	2	289	c.187G>A	c.(187-189)GTG>ATG	p.V63M	TREM2_uc003opz.2_Missense_Mutation_p.V93M|TREM2_uc010jxl.1_Missense_Mutation_p.V93M	NM_018965	NP_061838	Q9NZC2	TREM2_HUMAN	triggering receptor expressed on myeloid cells 2	63	Ig-like V-type.|Extracellular (Potential).				axon guidance|humoral immune response	extracellular region|integral to membrane|plasma membrane	receptor activity			ovary(1)	1	Ovarian(28;0.0418)|Colorectal(47;0.196)																	---	---	---	---
USP49	25862	broad.mit.edu	37	6	41771563	41771563	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41771563G>A	uc003ori.2	-	5	1764	c.1542C>T	c.(1540-1542)TAC>TAT	p.Y514Y		NM_018561	NP_061031	Q70CQ1	UBP49_HUMAN	ubiquitin thioesterase 49	514					ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(28;0.0919)|Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000309)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)															---	---	---	---
UBR2	23304	broad.mit.edu	37	6	42629991	42629991	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42629991T>G	uc011dur.1	+	31	3512	c.3512T>G	c.(3511-3513)ATT>AGT	p.I1171S	UBR2_uc011dus.1_Missense_Mutation_p.I816S|UBR2_uc003osh.2_RNA	NM_015255	NP_056070	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin	1171	RING-type; atypical.				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)															---	---	---	---
PPP2R5D	5528	broad.mit.edu	37	6	42974208	42974208	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42974208C>A	uc003oth.2	+	3	199	c.113C>A	c.(112-114)CCG>CAG	p.P38Q	MEA1_uc010jyc.1_Intron|PPP2R5D_uc003otg.2_Missense_Mutation_p.P38Q|PPP2R5D_uc010jyd.2_Intron|PPP2R5D_uc011dva.1_Intron|PPP2R5D_uc003oti.2_5'UTR|PPP2R5D_uc003otj.2_5'Flank	NM_006245	NP_006236	Q14738	2A5D_HUMAN	delta isoform of regulatory subunit B56, protein	38	8 X 2 AA approximate tandem repeats of Q- P.|1.				nervous system development|signal transduction	cytoplasm|nucleus|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			breast(1)|central_nervous_system(1)	2			Colorectal(64;0.00237)|all cancers(41;0.00411)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0664)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)															---	---	---	---
RSPH9	221421	broad.mit.edu	37	6	43618211	43618211	+	Silent	SNP	C	T	T	rs140285713		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43618211C>T	uc003ovw.1	+	2	353	c.327C>T	c.(325-327)TAC>TAT	p.Y109Y	RSPH9_uc003ovx.1_Silent_p.Y109Y	NM_152732	NP_689945	Q9H1X1	RSPH9_HUMAN	radial spoke head 9 homolog	109					cilium axoneme assembly|cilium movement	cytoplasm|cytoskeleton				upper_aerodigestive_tract(1)|skin(1)	2														Kartagener_syndrome				---	---	---	---
AARS2	57505	broad.mit.edu	37	6	44268412	44268412	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44268412G>A	uc010jza.1	-	22	2833	c.2830C>T	c.(2830-2832)CTG>TTG	p.L944L	SPATS1_uc003oxg.2_Intron|TMEM151B_uc003oxf.2_Intron|TCTE1_uc003oxi.2_5'Flank	NM_020745	NP_065796	Q5JTZ9	SYAM_HUMAN	alanyl-tRNA synthetase 2, mitochondrial	944					alanyl-tRNA aminoacylation	mitochondrion	alanine-tRNA ligase activity|ATP binding|metal ion binding|tRNA binding			ovary(1)	1	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)		L-Alanine(DB00160)													---	---	---	---
GPR116	221395	broad.mit.edu	37	6	46834745	46834745	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46834745C>G	uc003oyo.3	-	13	2040	c.1751G>C	c.(1750-1752)GGT>GCT	p.G584A	GPR116_uc011dwj.1_Missense_Mutation_p.G139A|GPR116_uc011dwk.1_Missense_Mutation_p.G13A|GPR116_uc003oyp.3_Missense_Mutation_p.G442A|GPR116_uc003oyq.3_Missense_Mutation_p.G584A|GPR116_uc010jzi.1_Missense_Mutation_p.G256A	NM_001098518	NP_001091988	Q8IZF2	GP116_HUMAN	G-protein coupled receptor 116 precursor	584	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(1)|skin(1)	2			Lung(136;0.192)															---	---	---	---
FBXO9	26268	broad.mit.edu	37	6	52957243	52957243	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52957243C>T	uc003pbo.2	+	8	751	c.700C>T	c.(700-702)CGT>TGT	p.R234C	FBXO9_uc003pbk.2_Missense_Mutation_p.R190C|FBXO9_uc003pbl.2_Missense_Mutation_p.R224C|FBXO9_uc003pbm.2_Missense_Mutation_p.R114C|FBXO9_uc003pbn.2_Missense_Mutation_p.R114C	NM_012347	NP_036479	Q9UK97	FBX9_HUMAN	F-box only protein 9 isoform 1	234	F-box.					ubiquitin ligase complex	ubiquitin-protein ligase activity			pancreas(1)	1	Lung NSC(77;0.103)																	---	---	---	---
FAM83B	222584	broad.mit.edu	37	6	54805046	54805046	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54805046C>T	uc003pck.2	+	5	1393	c.1277C>T	c.(1276-1278)GCG>GTG	p.A426V		NM_001010872	NP_001010872	Q5T0W9	FA83B_HUMAN	hypothetical protein LOC222584	426										ovary(6)	6	Lung NSC(77;0.0178)|Renal(3;0.122)																	---	---	---	---
LGSN	51557	broad.mit.edu	37	6	63990392	63990392	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63990392A>G	uc003peh.2	-	4	1098	c.1064T>C	c.(1063-1065)CTC>CCC	p.L355P	LGSN_uc003pei.2_3'UTR	NM_016571	NP_057655	Q5TDP6	LGSN_HUMAN	lengsin, lens protein with glutamine synthetase	355					glutamine biosynthetic process		glutamate-ammonia ligase activity			skin(2)	2					L-Glutamic Acid(DB00142)													---	---	---	---
PHF3	23469	broad.mit.edu	37	6	64395006	64395006	+	Silent	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64395006C>A	uc003pep.1	+	3	1409	c.1383C>A	c.(1381-1383)TCC>TCA	p.S461S	PHF3_uc010kaf.1_Silent_p.S461S|PHF3_uc003pem.2_Silent_p.S414S|PHF3_uc010kag.1_Silent_p.S373S|PHF3_uc010kah.1_Silent_p.S275S|PHF3_uc003pen.2_Silent_p.S373S|PHF3_uc011dxs.1_Intron|PHF3_uc003peo.2_Silent_p.S461S	NM_015153	NP_055968	Q92576	PHF3_HUMAN	PHD finger protein 3	461					multicellular organismal development|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)															---	---	---	---
HTR1B	3351	broad.mit.edu	37	6	78172363	78172363	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:78172363C>T	uc003pil.1	-	1	758	c.758G>A	c.(757-759)CGA>CAA	p.R253Q		NM_000863	NP_000854	P28222	5HT1B_HUMAN	5-hydroxytryptamine (serotonin) receptor 1B	253	Cytoplasmic (By similarity).				G-protein signaling, coupled to cyclic nucleotide second messenger|negative regulation of cAMP biosynthetic process|synaptic transmission	integral to plasma membrane	protein binding|serotonin receptor activity				0		all_cancers(76;0.0867)|Acute lymphoblastic leukemia(125;0.00119)|all_hematologic(105;0.0332)		BRCA - Breast invasive adenocarcinoma(397;0.205)	Almotriptan(DB00918)|Dexfenfluramine(DB01191)|Dihydroergotamine(DB00320)|Eletriptan(DB00216)|Ergotamine(DB00696)|Frovatriptan(DB00998)|Naratriptan(DB00952)|Pindolol(DB00960)|Propranolol(DB00571)|Rizatriptan(DB00953)|Sumatriptan(DB00669)|Venlafaxine(DB00285)|Zolmitriptan(DB00315)													---	---	---	---
HTR1E	3354	broad.mit.edu	37	6	87725545	87725545	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87725545C>T	uc003pli.2	+	2	1196	c.493C>T	c.(493-495)CGC>TGC	p.R165C		NM_000865	NP_000856	P28566	5HT1E_HUMAN	5-hydroxytryptamine (serotonin) receptor 1E	165	Extracellular (By similarity).				G-protein signaling, coupled to cyclic nucleotide second messenger|synaptic transmission	integral to plasma membrane	protein binding|serotonin binding|serotonin receptor activity			ovary(2)|skin(1)	3		all_cancers(76;7.11e-06)|Acute lymphoblastic leukemia(125;1.2e-09)|Prostate(29;3.51e-09)|all_hematologic(105;7.43e-06)|all_epithelial(107;0.00819)		BRCA - Breast invasive adenocarcinoma(108;0.055)	Eletriptan(DB00216)													---	---	---	---
ZNF292	23036	broad.mit.edu	37	6	87970660	87970660	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87970660C>T	uc003plm.3	+	8	7354	c.7313C>T	c.(7312-7314)ACG>ATG	p.T2438M		NM_015021	NP_055836	O60281	ZN292_HUMAN	zinc finger protein 292	2438					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)														---	---	---	---
MDN1	23195	broad.mit.edu	37	6	90390385	90390385	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90390385C>T	uc003pnn.1	-	74	12304	c.12188G>A	c.(12187-12189)CGC>CAC	p.R4063H		NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog	4063					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	90513142	90513142	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90513142T>G	uc003pnn.1	-	2	350	c.234A>C	c.(232-234)GAA>GAC	p.E78D	MDN1_uc003pnp.1_Missense_Mutation_p.E78D	NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog	78					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	90573875	90573875	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90573875T>G	uc003pnr.2	+	7	2643	c.2447T>G	c.(2446-2448)CTT>CGT	p.L816R	CASP8AP2_uc003pns.2_Intron|CASP8AP2_uc003pnt.2_Missense_Mutation_p.L816R|CASP8AP2_uc011dzz.1_Missense_Mutation_p.L816R	NM_001137667	NP_001131139	Q9UKL3	C8AP2_HUMAN	caspase 8 associated protein 2	816					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)														---	---	---	---
HACE1	57531	broad.mit.edu	37	6	105198313	105198313	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105198313A>G	uc003pqu.1	-	20	2523	c.2246T>C	c.(2245-2247)ATG>ACG	p.M749T	HACE1_uc010kcy.1_Missense_Mutation_p.M231T|HACE1_uc010kcz.1_Missense_Mutation_p.M534T|HACE1_uc010kcx.1_Missense_Mutation_p.M158T|HACE1_uc003pqt.1_Missense_Mutation_p.M402T	NM_020771	NP_065822	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing, E3	749	HECT.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	endoplasmic reticulum	ubiquitin-protein ligase activity			ovary(5)|lung(2)	7		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)														---	---	---	---
ARMC2	84071	broad.mit.edu	37	6	109249304	109249304	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109249304T>C	uc003pss.3	+	11	1538	c.1364T>C	c.(1363-1365)TTG>TCG	p.L455S	ARMC2_uc011eao.1_Missense_Mutation_p.L290S	NM_032131	NP_115507	Q8NEN0	ARMC2_HUMAN	armadillo repeat containing 2	455							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)														---	---	---	---
C6orf182	285753	broad.mit.edu	37	6	109484118	109484118	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109484118G>A	uc010kdk.2	+	13	1905	c.1328G>A	c.(1327-1329)CGA>CAA	p.R443Q	C6orf182_uc003psx.3_3'UTR|C6orf182_uc010kdl.2_Missense_Mutation_p.R443Q|C6orf182_uc003psy.3_Missense_Mutation_p.R443Q	NM_001083535	NP_001077004	Q8IYX8	CE57L_HUMAN	hypothetical protein LOC285753	443						microtubule|microtubule organizing center					0		all_cancers(87;4.45e-07)|Acute lymphoblastic leukemia(125;2.15e-10)|all_hematologic(75;3.25e-08)|all_epithelial(87;0.000254)|Colorectal(196;0.0293)|all_lung(197;0.11)		BRCA - Breast invasive adenocarcinoma(108;0.00123)|Epithelial(106;0.0022)|all cancers(137;0.00405)|OV - Ovarian serous cystadenocarcinoma(136;0.0233)														---	---	---	---
CDC40	51362	broad.mit.edu	37	6	110534359	110534359	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110534359T>G	uc003pua.2	+	8	962	c.938T>G	c.(937-939)ATT>AGT	p.I313S		NM_015891	NP_056975	O60508	PRP17_HUMAN	cell division cycle 40 homolog	313	WD 1.				mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|nucleoplasm					0		all_cancers(87;6.23e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		Epithelial(106;0.0221)|all cancers(137;0.0314)|OV - Ovarian serous cystadenocarcinoma(136;0.034)														---	---	---	---
CDC40	51362	broad.mit.edu	37	6	110547426	110547426	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110547426C>T	uc003pua.2	+	13	1421	c.1397C>T	c.(1396-1398)GCA>GTA	p.A466V		NM_015891	NP_056975	O60508	PRP17_HUMAN	cell division cycle 40 homolog	466	WD 5.				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)														---	---	---	---
SLC35F1	222553	broad.mit.edu	37	6	118475711	118475711	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118475711C>T	uc003pxx.3	+	2	478	c.277C>T	c.(277-279)CCA>TCA	p.P93S		NM_001029858	NP_001025029	Q5T1Q4	S35F1_HUMAN	solute carrier family 35, member F1	93					transport	integral to membrane				breast(1)	1				GBM - Glioblastoma multiforme(226;0.217)														---	---	---	---
HSF2	3298	broad.mit.edu	37	6	122744779	122744779	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122744779A>C	uc003pyu.2	+	10	1311	c.1124A>C	c.(1123-1125)CAG>CCG	p.Q375P	HSF2_uc003pyv.2_Missense_Mutation_p.Q375P	NM_004506	NP_004497	Q03933	HSF2_HUMAN	heat shock transcription factor 2 isoform a	375	Hydrophobic repeat HR-C.				response to stress|transcription from RNA polymerase II promoter	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription coactivator activity				0				OV - Ovarian serous cystadenocarcinoma(136;0.00371)|all cancers(137;0.0299)|GBM - Glioblastoma multiforme(226;0.0586)														---	---	---	---
C6orf174	387104	broad.mit.edu	37	6	127796467	127796467	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127796467C>T	uc003qbd.2	-	6	3569	c.2704G>A	c.(2704-2706)GGC>AGC	p.G902S	C6orf174_uc003qbc.2_5'UTR	NM_001012279	NP_001012279	Q5TF21	CF174_HUMAN	hypothetical protein LOC387104 precursor	902						integral to membrane				breast(3)|ovary(2)|skin(1)	6				GBM - Glioblastoma multiforme(226;0.026)|all cancers(137;0.161)														---	---	---	---
HBS1L	10767	broad.mit.edu	37	6	135287504	135287504	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135287504T>C	uc003qez.2	-	17	2213	c.2006A>G	c.(2005-2007)TAC>TGC	p.Y669C	HBS1L_uc003qey.2_Missense_Mutation_p.Y505C|HBS1L_uc011ecy.1_Missense_Mutation_p.Y393C|HBS1L_uc011ecz.1_Missense_Mutation_p.Y505C|HBS1L_uc011eda.1_Missense_Mutation_p.Y627C	NM_006620	NP_006611	Q9Y450	HBS1L_HUMAN	Hsp70 subfamily B suppressor 1-like protein	669					signal transduction		GTP binding|GTPase activity|translation elongation factor activity			skin(2)	2	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)														---	---	---	---
KIAA1244	57221	broad.mit.edu	37	6	138656207	138656207	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138656207A>G	uc003qhu.2	+	33	6224	c.6224A>G	c.(6223-6225)CAA>CGA	p.Q2075R		NM_020340	NP_065073	Q5TH69	BIG3_HUMAN	brefeldin A-inhibited guanine	2075					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	139488098	139488098	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139488098T>G	uc003qin.2	+	2	1234	c.949T>G	c.(949-951)TTC>GTC	p.F317V		NM_016217	NP_057301	Q9UBI9	HDC_HUMAN	headcase	317					respiratory tube development						0				GBM - Glioblastoma multiforme(68;0.000252)|OV - Ovarian serous cystadenocarcinoma(155;0.000387)														---	---	---	---
TXLNB	167838	broad.mit.edu	37	6	139564163	139564163	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139564163G>T	uc011eds.1	-	10	1720	c.1555C>A	c.(1555-1557)CAG>AAG	p.Q519K		NM_153235	NP_694967	Q8N3L3	TXLNB_HUMAN	taxilin beta	519						cytoplasm				large_intestine(1)|ovary(1)	2				OV - Ovarian serous cystadenocarcinoma(155;0.000185)|GBM - Glioblastoma multiforme(68;0.000235)														---	---	---	---
UTRN	7402	broad.mit.edu	37	6	144872230	144872230	+	Intron	SNP	A	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144872230A>T	uc003qkt.2	+							NM_007124	NP_009055			utrophin						muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)														---	---	---	---
SHPRH	257218	broad.mit.edu	37	6	146243890	146243890	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146243890C>T	uc003qlf.2	-	19	4027	c.3628G>A	c.(3628-3630)GCT>ACT	p.A1210T	SHPRH_uc003qld.2_Missense_Mutation_p.A1214T|SHPRH_uc003qle.2_Missense_Mutation_p.A1214T|SHPRH_uc003qlg.1_Missense_Mutation_p.A766T|SHPRH_uc003qlh.2_Missense_Mutation_p.A135T|SHPRH_uc003qli.1_Missense_Mutation_p.A135T	NM_001042683	NP_001036148	Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase isoform a	1210					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	146256278	146256278	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146256278C>T	uc003qlf.2	-	13	3154	c.2755G>A	c.(2755-2757)GAA>AAA	p.E919K	SHPRH_uc003qld.2_Missense_Mutation_p.E919K|SHPRH_uc003qle.2_Missense_Mutation_p.E919K|SHPRH_uc003qlg.1_Missense_Mutation_p.E475K|SHPRH_uc003qlj.1_Missense_Mutation_p.E808K|SHPRH_uc003qlh.2_5'Flank	NM_001042683	NP_001036148	Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase isoform a	919					DNA repair|nucleosome assembly	nucleosome|nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)|kidney(1)|central_nervous_system(1)	3		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)														---	---	---	---
STXBP5	134957	broad.mit.edu	37	6	147636770	147636770	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147636770T>C	uc003qlz.2	+	15	1683	c.1522T>C	c.(1522-1524)TCC>CCC	p.S508P	STXBP5_uc010khz.1_Missense_Mutation_p.S508P|STXBP5_uc003qlx.2_RNA|STXBP5_uc003qly.2_Missense_Mutation_p.S179P	NM_001127715	NP_001121187	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn) isoform b	508	WD 9.				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)														---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152555065	152555065	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152555065G>T	uc010kiw.2	-	112	21165	c.20563C>A	c.(20563-20565)CTG>ATG	p.L6855M	SYNE1_uc010kiv.2_Missense_Mutation_p.L1379M|SYNE1_uc003qos.3_Missense_Mutation_p.L1379M|SYNE1_uc003qot.3_Missense_Mutation_p.L6784M|SYNE1_uc003qou.3_Missense_Mutation_p.L6855M	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	6855	Spectrin 21.|Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)											HNSCC(10;0.0054)			---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152599278	152599278	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152599278C>A	uc010kiw.2	-	98	19121	c.18519G>T	c.(18517-18519)AAG>AAT	p.K6173N	SYNE1_uc010kiv.2_Missense_Mutation_p.K697N|SYNE1_uc003qos.3_Missense_Mutation_p.K697N|SYNE1_uc003qot.3_Missense_Mutation_p.K6102N|SYNE1_uc003qou.3_Missense_Mutation_p.K6173N|SYNE1_uc010kiy.1_Missense_Mutation_p.K352N	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	6173	Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)											HNSCC(10;0.0054)			---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152631934	152631934	+	Silent	SNP	G	A	A	rs142010074		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152631934G>A	uc010kiw.2	-	88	17387	c.16785C>T	c.(16783-16785)AGC>AGT	p.S5595S	SYNE1_uc010kiv.2_Silent_p.S119S|SYNE1_uc003qos.3_Silent_p.S119S|SYNE1_uc003qot.3_Silent_p.S5524S|SYNE1_uc003qou.3_Silent_p.S5595S	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5595	Spectrin 17.|Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)											HNSCC(10;0.0054)			---	---	---	---
RBM16	22828	broad.mit.edu	37	6	155131196	155131196	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155131196G>A	uc003qqa.2	+	13	1506	c.1274G>A	c.(1273-1275)CGT>CAT	p.R425H	RBM16_uc011efj.1_Missense_Mutation_p.R491H|RBM16_uc011efk.1_Missense_Mutation_p.R470H|RBM16_uc003qpz.2_Missense_Mutation_p.R425H|RBM16_uc010kji.2_Missense_Mutation_p.R446H	NM_014892	NP_055707	Q9UPN6	SCAF8_HUMAN	RNA-binding motif protein 16	425	Arg-rich.				mRNA processing|RNA splicing	nuclear matrix|spliceosomal complex	nucleotide binding|RNA binding|RNA polymerase core enzyme binding				0		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;2.33e-15)|BRCA - Breast invasive adenocarcinoma(81;0.00524)														---	---	---	---
TIAM2	26230	broad.mit.edu	37	6	155504445	155504445	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155504445G>A	uc003qqb.2	+	16	4148	c.2875G>A	c.(2875-2877)GCC>ACC	p.A959T	TIAM2_uc003qqe.2_Missense_Mutation_p.A959T|TIAM2_uc010kjj.2_Missense_Mutation_p.A492T|TIAM2_uc003qqf.2_Missense_Mutation_p.A335T|TIAM2_uc011efl.1_Missense_Mutation_p.A295T|TIAM2_uc003qqg.2_Missense_Mutation_p.A271T	NM_012454	NP_036586	Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	959	PDZ.				apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)														---	---	---	---
TMEM181	57583	broad.mit.edu	37	6	159046206	159046206	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159046206C>T	uc003qrm.3	+	12	1447	c.1436C>T	c.(1435-1437)GCG>GTG	p.A479V	TMEM181_uc010kjr.1_Missense_Mutation_p.A310V	NM_020823	NP_065874	Q9P2C4	TM181_HUMAN	G protein-coupled receptor 178	479					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)														---	---	---	---
SOD2	6648	broad.mit.edu	37	6	160105942	160105942	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160105942C>T	uc003qsg.2	-	4	621	c.467G>A	c.(466-468)CGG>CAG	p.R156Q	SOD2_uc003qsh.2_Missense_Mutation_p.R117Q|SOD2_uc003qsi.1_Missense_Mutation_p.R156Q|SOD2_uc011efu.1_Intron|SOD2_uc011efv.1_Missense_Mutation_p.R117Q	NM_001024465	NP_001019636	P04179	SODM_HUMAN	manganese superoxide dismutase isoform A	156					age-dependent response to reactive oxygen species|negative regulation of neuron apoptosis|oxygen homeostasis|protein homotetramerization|regulation of transcription from RNA polymerase II promoter|release of cytochrome c from mitochondria|removal of superoxide radicals|vasodilation by acetylcholine involved in regulation of systemic arterial blood pressure		manganese ion binding|superoxide dismutase activity				0		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.103)		OV - Ovarian serous cystadenocarcinoma(65;1.4e-18)|BRCA - Breast invasive adenocarcinoma(81;5.77e-06)														---	---	---	---
PNLDC1	154197	broad.mit.edu	37	6	160237067	160237067	+	Splice_Site	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160237067T>G	uc003qsx.1	+	13	1198	c.1027_splice	c.e13+2	p.V343_splice	PNLDC1_uc003qsy.1_Splice_Site_p.V354_splice	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)														---	---	---	---
LPA	4018	broad.mit.edu	37	6	160998216	160998216	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160998216G>T	uc003qtl.2	-	29	4703	c.4583C>A	c.(4582-4584)TCT>TAT	p.S1528Y		NM_005577	NP_005568	P08519	APOA_HUMAN	lipoprotein Lp(a) precursor	4036	Kringle 36.				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	163149390	163149390	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163149390T>C	uc003qua.2	+	2	347	c.123T>C	c.(121-123)GGT>GGC	p.G41G	PARK2_uc003qtx.3_5'Flank|PARK2_uc003qty.3_5'Flank|PARK2_uc003qtz.3_5'Flank|PARK2_uc010kke.1_5'Flank|PACRG_uc003qub.2_Silent_p.G41G|PACRG_uc003quc.2_Silent_p.G41G	NM_152410	NP_689623	Q96M98	PACRG_HUMAN	parkin co-regulated gene protein isoform 1	41											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)														---	---	---	---
FGFR1OP	11116	broad.mit.edu	37	6	167413595	167413595	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167413595A>G	uc003qvj.2	+	2	235	c.150A>G	c.(148-150)AAA>AAG	p.K50K	RNASET2_uc003qvh.2_5'Flank|CCR6_uc003qvl.2_5'UTR|FGFR1OP_uc011egp.1_Silent_p.K50K|FGFR1OP_uc003qvk.2_Silent_p.K50K	NM_007045	NP_008976	O95684	FR1OP_HUMAN	FGFR1 oncogene partner isoform a	50					G2/M transition of mitotic cell cycle|microtubule anchoring|positive regulation of cell growth|positive regulation of cell migration|positive regulation of cell proliferation	centrosome|cytosol|nucleus|perinuclear region of cytoplasm	protein homodimerization activity|protein kinase binding|protein tyrosine kinase inhibitor activity			ovary(1)	1		Breast(66;1.48e-05)|Ovarian(120;0.0607)		OV - Ovarian serous cystadenocarcinoma(33;1.73e-19)|BRCA - Breast invasive adenocarcinoma(81;5.1e-06)|GBM - Glioblastoma multiforme(31;0.00231)				T	FGFR1	MPD|NHL								---	---	---	---
PHF10	55274	broad.mit.edu	37	6	170105294	170105294	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170105294A>G	uc011egy.1	-	11	1425	c.1346T>C	c.(1345-1347)ATG>ACG	p.M449T	C6orf120_uc003qxb.2_3'UTR|PHF10_uc011egz.1_Missense_Mutation_p.M447T	NM_018288	NP_060758	Q8WUB8	PHF10_HUMAN	PHD finger protein 10 isoform a	449	PHD-type 2; degenerate.				nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	npBAF complex	zinc ion binding			urinary_tract(1)	1		Breast(66;5.08e-05)|Ovarian(120;0.208)		OV - Ovarian serous cystadenocarcinoma(33;1.4e-21)|BRCA - Breast invasive adenocarcinoma(81;1.4e-07)|GBM - Glioblastoma multiforme(31;0.00176)														---	---	---	---
TMEM184A	202915	broad.mit.edu	37	7	1590504	1590504	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1590504C>T	uc003skv.3	-	3	651	c.334G>A	c.(334-336)GGA>AGA	p.G112R	TMEM184A_uc003skt.3_5'UTR|TMEM184A_uc003skw.3_5'UTR	NM_001097620	NP_001091089	Q6ZMB5	T184A_HUMAN	transmembrane protein 184A	112	Helical; (Potential).					integral to membrane					0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;5.88e-15)														---	---	---	---
KIAA0415	9907	broad.mit.edu	37	7	4820880	4820880	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4820880C>T	uc003sne.2	+	2	199	c.116C>T	c.(115-117)CCG>CTG	p.P39L	KIAA0415_uc010ksp.2_RNA	NM_014855	NP_055670	O43299	K0415_HUMAN	hypothetical protein LOC9907	39					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)														---	---	---	---
RADIL	55698	broad.mit.edu	37	7	4839057	4839057	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4839057G>A	uc003snj.1	-	15	3353	c.3180C>T	c.(3178-3180)TCC>TCT	p.S1060S	RADIL_uc003sng.1_RNA|RADIL_uc003sni.1_Silent_p.S565S|RADIL_uc011jwc.1_Silent_p.S820S|RADIL_uc011jwd.1_RNA|RADIL_uc003snh.1_Silent_p.S356S	NM_018059	NP_060529	Q96JH8	RADIL_HUMAN	Rap GTPase interactor	1060	PDZ.				cell adhesion|multicellular organismal development|signal transduction		protein binding			lung(2)|central_nervous_system(2)|pancreas(2)|breast(1)	7		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)														---	---	---	---
LOC389458	389458	broad.mit.edu	37	7	5112605	5112605	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5112605G>T	uc003snr.2	+	8	801	c.488G>T	c.(487-489)CGG>CTG	p.R163L	LOC389458_uc010kst.2_Silent_p.P57P					Synthetic construct DNA, clone: pF1KB3788, Homo sapiens RBAK gene for RB-associated KRAB repressor, complete cds, without stop codon, in Flexi system.												0																		---	---	---	---
WIPI2	26100	broad.mit.edu	37	7	5232740	5232740	+	Intron	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5232740T>G	uc003snv.2	+						WIPI2_uc003snw.2_Intron|WIPI2_uc003snx.2_Intron|WIPI2_uc003sny.2_Intron|WIPI2_uc010ksv.2_Intron	NM_015610	NP_056425			WD repeat domain, phosphoinositide interacting 2						autophagic vacuole assembly	cytosol|PAS complex|pre-autophagosomal structure membrane	phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding			ovary(2)	2		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0925)|OV - Ovarian serous cystadenocarcinoma(56;2.59e-14)														---	---	---	---
RNF216	54476	broad.mit.edu	37	7	5778933	5778933	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5778933A>T	uc003soy.1	-	5	1114	c.924T>A	c.(922-924)CAT>CAA	p.H308Q	RNF216_uc010ksz.1_5'UTR|RNF216_uc010kta.1_Intron|RNF216_uc011jwj.1_Intron|RNF216_uc003sox.1_Missense_Mutation_p.H365Q	NM_207116	NP_996999	Q9NWF9	RN216_HUMAN	ring finger protein 216 isoform b	308					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)														---	---	---	---
C7orf28A	51622	broad.mit.edu	37	7	5941347	5941347	+	Intron	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5941347G>A	uc003spf.2	+							NM_015622	NP_056437			hypothetical protein LOC51622							lysosomal membrane					0		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0974)|OV - Ovarian serous cystadenocarcinoma(56;7.91e-15)														---	---	---	---
PMS2	5395	broad.mit.edu	37	7	6026972	6026972	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6026972A>G	uc003spl.2	-	11	1511	c.1424T>C	c.(1423-1425)GTG>GCG	p.V475A	PMS2_uc003spj.2_Missense_Mutation_p.V369A|PMS2_uc003spk.2_Missense_Mutation_p.V340A|PMS2_uc011jwl.1_Missense_Mutation_p.V340A|PMS2_uc010ktg.2_Missense_Mutation_p.V164A|PMS2_uc010kte.2_Intron|PMS2_uc010ktf.1_Missense_Mutation_p.V475A	NM_000535	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 isoform	475					mismatch repair|reciprocal meiotic recombination|somatic hypermutation of immunoglobulin genes	MutLalpha complex	ATP binding|ATPase activity|endonuclease activity|protein binding|single base insertion or deletion binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)				Mis|N|F			colorectal|endometrial|ovarian|medulloblastoma|glioma		Direct_reversal_of_damage|MMR	Lynch_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				---	---	---	---
C7orf70	84792	broad.mit.edu	37	7	6370054	6370054	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6370054T>C	uc003spu.2	-	2	1200	c.732A>G	c.(730-732)TTA>TTG	p.L244L		NM_001037163	NP_001032240	Q7Z4H9	SIPAR_HUMAN	hypothetical protein LOC84792	244						nucleus					0																		---	---	---	---
ZNF12	7559	broad.mit.edu	37	7	6731113	6731113	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6731113T>C	uc003sqt.1	-	5	2014	c.1460A>G	c.(1459-1461)CAC>CGC	p.H487R	ZNF12_uc011jxa.1_Missense_Mutation_p.H325R|ZNF12_uc003sqs.1_Missense_Mutation_p.H449R	NM_016265	NP_057349	P17014	ZNF12_HUMAN	zinc finger protein 12 isoform a	487	C2H2-type 8.				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)														---	---	---	---
FERD3L	222894	broad.mit.edu	37	7	19184718	19184718	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:19184718C>A	uc003suo.1	-	1	327	c.268G>T	c.(268-270)GGC>TGC	p.G90C	uc003sun.1_RNA	NM_152898	NP_690862	Q96RJ6	FER3L_HUMAN	nephew of atonal 3	90					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			large_intestine(1)	1																		---	---	---	---
HOXA5	3202	broad.mit.edu	37	7	27181581	27181581	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27181581G>A	uc003syn.1	-	2	747	c.686C>T	c.(685-687)GCA>GTA	p.A229V		NM_019102	NP_061975	P20719	HXA5_HUMAN	homeobox A5	229	Homeobox.				negative regulation of angiogenesis|negative regulation of erythrocyte differentiation|positive regulation of apoptosis|positive regulation of myeloid cell differentiation|positive regulation of receptor biosynthetic process|positive regulation of transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																OREG0017911	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CPVL	54504	broad.mit.edu	37	7	29134731	29134731	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29134731G>A	uc003szv.2	-	5	550	c.431C>T	c.(430-432)ACA>ATA	p.T144I	CPVL_uc003szw.2_Missense_Mutation_p.T144I|CPVL_uc003szx.2_Missense_Mutation_p.T144I	NM_031311	NP_112601	Q9H3G5	CPVL_HUMAN	serine carboxypeptidase vitellogenic-like	144					proteolysis		protein binding|serine-type carboxypeptidase activity			ovary(2)	2																		---	---	---	---
SCRN1	9805	broad.mit.edu	37	7	29976289	29976289	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29976289C>T	uc010kvp.2	-	5	992	c.788G>A	c.(787-789)AGC>AAC	p.S263N	SCRN1_uc011jzy.1_Missense_Mutation_p.S195N|SCRN1_uc003tak.2_Missense_Mutation_p.S263N|SCRN1_uc011jzz.1_Missense_Mutation_p.S263N|SCRN1_uc011kaa.1_Missense_Mutation_p.S283N|SCRN1_uc011jzw.1_Missense_Mutation_p.S130N|SCRN1_uc011jzx.1_Missense_Mutation_p.S86N	NM_001145515	NP_001138987	Q12765	SCRN1_HUMAN	secernin 1 isoform c	263					exocytosis|proteolysis	cytoplasm|nuclear membrane	dipeptidase activity			ovary(2)	2																		---	---	---	---
ADCYAP1R1	117	broad.mit.edu	37	7	31142845	31142845	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31142845C>T	uc003tca.1	+						ADCYAP1R1_uc003tcb.1_Intron|ADCYAP1R1_uc003tcc.1_Intron|ADCYAP1R1_uc003tcd.1_Intron|ADCYAP1R1_uc003tce.1_Intron|ADCYAP1R1_uc003tcf.1_Intron	NM_001118	NP_001109			adenylate cyclase activating polypeptide 1						activation of adenylate cyclase activity|cell differentiation|nerve growth factor receptor signaling pathway|spermatogenesis	integral to plasma membrane	vasoactive intestinal polypeptide receptor activity			ovary(1)	1																		---	---	---	---
GPR141	353345	broad.mit.edu	37	7	37780523	37780523	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37780523A>G	uc003tfm.1	+	1	528	c.528A>G	c.(526-528)ACA>ACG	p.T176T	uc003tfl.2_Intron	NM_181791	NP_861456	Q7Z602	GP141_HUMAN	G protein-coupled receptor 141	176	Extracellular (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)	3																		---	---	---	---
GPR141	353345	broad.mit.edu	37	7	37780806	37780806	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37780806A>G	uc003tfm.1	+	1	811	c.811A>G	c.(811-813)AGT>GGT	p.S271G	uc003tfl.2_Intron	NM_181791	NP_861456	Q7Z602	GP141_HUMAN	G protein-coupled receptor 141	271	Helical; Name=7; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	38393734	38393734	+	Intron	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38393734G>A	uc003tgp.1	+											Homo sapiens cDNA FLJ43658 fis, clone SYNOV4004184.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	38402569	38402569	+	Intron	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38402569C>A	uc003tgp.1	+						uc003tgs.1_Missense_Mutation_p.G84W					Homo sapiens cDNA FLJ43658 fis, clone SYNOV4004184.																														---	---	---	---
INHBA	3624	broad.mit.edu	37	7	41729268	41729268	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41729268C>T	uc003thq.2	-	2	1496	c.1261G>A	c.(1261-1263)GAG>AAG	p.E421K	INHBA_uc003thr.2_Missense_Mutation_p.E421K	NM_002192	NP_002183	P08476	INHBA_HUMAN	inhibin beta A precursor	421					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)			---	---	---	---
ZMIZ2	83637	broad.mit.edu	37	7	44805885	44805885	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44805885A>G	uc003tlr.2	+	17	2488	c.2365A>G	c.(2365-2367)AGC>GGC	p.S789G	ZMIZ2_uc003tlq.2_Missense_Mutation_p.S731G|ZMIZ2_uc003tls.2_Missense_Mutation_p.S763G|ZMIZ2_uc003tlt.2_Missense_Mutation_p.S412G|ZMIZ2_uc010kyj.2_Missense_Mutation_p.S311G|ZMIZ2_uc003tlu.2_Missense_Mutation_p.S70G|ZMIZ2_uc010kyk.1_5'Flank	NM_031449	NP_113637	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2 isoform 1	789	Pro-rich.				positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear replication fork	ligand-dependent nuclear receptor transcription coactivator activity|protein binding|zinc ion binding			ovary(2)|large_intestine(2)|breast(1)	5																		---	---	---	---
ASL	435	broad.mit.edu	37	7	65557009	65557009	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65557009T>C	uc003tuo.2	+	15	1190	c.1079T>C	c.(1078-1080)ATG>ACG	p.M360T	ASL_uc003tup.2_Missense_Mutation_p.M360T|ASL_uc003tur.2_Missense_Mutation_p.M334T|ASL_uc003tuq.2_Missense_Mutation_p.M340T	NM_000048	NP_000039	P04424	ARLY_HUMAN	argininosuccinate lyase isoform 1	360					arginine biosynthetic process via ornithine|arginine catabolic process|urea cycle	cytosol	argininosuccinate lyase activity			breast(2)	2					L-Arginine(DB00125)													---	---	---	---
FKBP6	8468	broad.mit.edu	37	7	72743394	72743394	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72743394C>T	uc003tya.2	+	3	339	c.207C>T	c.(205-207)GAC>GAT	p.D69D	FKBP6_uc003twz.2_Intron|FKBP6_uc011kew.1_Silent_p.D64D|FKBP6_uc010lbe.1_RNA|TRIM50_uc003txy.1_5'Flank|TRIM50_uc003txz.1_5'Flank	NM_003602	NP_003593	O75344	FKBP6_HUMAN	FK506 binding protein 6 isoform a	69	PPIase FKBP-type.				protein folding	membrane	FK506 binding|peptidyl-prolyl cis-trans isomerase activity				0		Lung NSC(55;0.0908)|all_lung(88;0.198)																---	---	---	---
BAZ1B	9031	broad.mit.edu	37	7	72865220	72865220	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72865220A>G	uc003tyc.2	-	14	3882	c.3537T>C	c.(3535-3537)GAT>GAC	p.D1179D		NM_032408	NP_115784	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	1179					ATP-dependent chromatin remodeling|chromatin-mediated maintenance of transcription|DNA replication-dependent nucleosome disassembly|double-strand break repair|heart morphogenesis|transcription, DNA-dependent	WINAC complex	ATP binding|chromatin binding|histone acetyl-lysine binding|histone kinase activity|non-membrane spanning protein tyrosine kinase activity|protein complex scaffold|vitamin D receptor activator activity|vitamin D receptor binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	7		Lung NSC(55;0.0659)|all_lung(88;0.152)																---	---	---	---
CLIP2	7461	broad.mit.edu	37	7	73770865	73770865	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73770865C>T	uc003uam.2	+	5	1256	c.929C>T	c.(928-930)GCA>GTA	p.A310V	CLIP2_uc003uan.2_Missense_Mutation_p.A310V	NM_003388	NP_003379	Q9UDT6	CLIP2_HUMAN	CAP-GLY domain containing linker protein 2	310						microtubule associated complex				skin(3)	3																		---	---	---	---
SRCRB4D	136853	broad.mit.edu	37	7	76028048	76028048	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76028048G>A	uc003ufb.2	-	5	890	c.542C>T	c.(541-543)CCG>CTG	p.P181L	ZP3_uc003ufc.3_Intron	NM_080744	NP_542782	Q8WTU2	SRB4D_HUMAN	scavenger receptor cysteine rich domain	181						extracellular region|membrane	scavenger receptor activity			pancreas(1)	1																		---	---	---	---
PION	54103	broad.mit.edu	37	7	77026294	77026294	+	Intron	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77026294A>G	uc003ugf.2	-						PION_uc003ugg.1_Intron	NM_017439	NP_059135			pigeon homolog						beta-amyloid formation|regulation of proteolysis	trans-Golgi network	beta-amyloid binding			central_nervous_system(1)	1																		---	---	---	---
PCLO	27445	broad.mit.edu	37	7	82579814	82579814	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82579814C>T	uc003uhx.2	-	6	10379	c.10090G>A	c.(10090-10092)GCA>ACA	p.A3364T	PCLO_uc003uhv.2_Missense_Mutation_p.A3364T|PCLO_uc010lec.2_Missense_Mutation_p.A329T	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	3295					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	82586186	82586186	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82586186G>A	uc003uhx.2	-	5	4372	c.4083C>T	c.(4081-4083)AGC>AGT	p.S1361S	PCLO_uc003uhv.2_Silent_p.S1361S	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	1292					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7																		---	---	---	---
SEMA3D	223117	broad.mit.edu	37	7	84628770	84628770	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84628770C>T	uc003uic.2	-	17	2360	c.2320G>A	c.(2320-2322)GCT>ACT	p.A774T	SEMA3D_uc010led.2_Missense_Mutation_p.A774T|SEMA3D_uc003uib.2_Missense_Mutation_p.A413T	NM_152754	NP_689967	O95025	SEM3D_HUMAN	semaphorin 3D precursor	774					cell differentiation|nervous system development	extracellular region|membrane	receptor activity			ovary(3)|large_intestine(2)	5																		---	---	---	---
HEPACAM2	253012	broad.mit.edu	37	7	92848794	92848794	+	Intron	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92848794A>G	uc003umm.2	-						HEPACAM2_uc003uml.2_Missense_Mutation_p.V5A|HEPACAM2_uc010lff.2_Missense_Mutation_p.V5A|HEPACAM2_uc011khy.1_Intron	NM_001039372	NP_001034461			HEPACAM family member 2 isoform 1							integral to membrane				ovary(3)|breast(1)|kidney(1)	5																		---	---	---	---
ASNS	440	broad.mit.edu	37	7	97488558	97488558	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97488558C>T	uc003uot.3	-	5	1146	c.640G>A	c.(640-642)GCC>ACC	p.A214T	ASNS_uc011kin.1_Missense_Mutation_p.A131T|ASNS_uc003uou.3_Missense_Mutation_p.A214T|ASNS_uc003uov.3_Missense_Mutation_p.A214T|ASNS_uc011kio.1_Missense_Mutation_p.A193T|ASNS_uc003uow.3_Missense_Mutation_p.A193T|ASNS_uc003uox.3_Missense_Mutation_p.A131T	NM_133436	NP_597680	P08243	ASNS_HUMAN	asparagine synthetase	214	Asparagine synthetase.				cellular response to glucose starvation|glutamine metabolic process|negative regulation of apoptosis|positive regulation of mitotic cell cycle	cytosol|soluble fraction	asparagine synthase (glutamine-hydrolyzing) activity|ATP binding			ovary(1)	1	all_cancers(62;6.64e-09)|all_epithelial(64;1.58e-09)|Esophageal squamous(72;0.00448)|Lung NSC(181;0.0342)|all_lung(186;0.0369)				Adenosine triphosphate(DB00171)|L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)|L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)													---	---	---	---
LMTK2	22853	broad.mit.edu	37	7	97823439	97823439	+	Missense_Mutation	SNP	G	A	A	rs150887629	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97823439G>A	uc003upd.1	+	11	3955	c.3662G>A	c.(3661-3663)CGC>CAC	p.R1221H		NM_014916	NP_055731	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2 precursor	1221					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)																	---	---	---	---
ZNF655	79027	broad.mit.edu	37	7	99171045	99171045	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99171045T>C	uc003urh.2	+	3	1707	c.1314T>C	c.(1312-1314)TGT>TGC	p.C438C	ZNF655_uc010lga.2_Silent_p.C473C|ZNF655_uc010lgc.2_Silent_p.C473C|ZNF655_uc003urj.2_Silent_p.C438C|ZNF655_uc003urk.2_Silent_p.C275C|ZNF655_uc010lgd.2_Silent_p.C275C	NM_138494	NP_612503	Q8N720	ZN655_HUMAN	zinc finger protein 655 isoform a	438					G1 phase|regulation of mitotic cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding|zinc ion binding			ovary(1)	1	all_epithelial(64;3.19e-09)|Lung NSC(181;0.0066)|all_lung(186;0.011)|Esophageal squamous(72;0.0166)																	---	---	---	---
PVRIG	79037	broad.mit.edu	37	7	99818284	99818284	+	Missense_Mutation	SNP	G	A	A	rs146047866	byFrequency	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99818284G>A	uc003uue.2	+	5	956	c.584G>A	c.(583-585)CGA>CAA	p.R195Q	GATS_uc003uty.3_Intron|GATS_uc003utz.3_Intron|GATS_uc003uua.3_Intron|GATS_uc010lgt.2_Intron|GATS_uc011kjl.1_Intron|GATS_uc010lgu.2_Intron|PVRIG_uc003uuf.1_Missense_Mutation_p.R195Q	NM_024070	NP_076975	Q6DKI7	PVRIG_HUMAN	poliovirus receptor related immunoglobulin	195						integral to membrane				skin(2)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
PVRIG	79037	broad.mit.edu	37	7	99818298	99818298	+	Splice_Site	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99818298T>C	uc003uue.2	+	5	968	c.596_splice	c.e5+2	p.R199_splice	GATS_uc003uty.3_Intron|GATS_uc003utz.3_Intron|GATS_uc003uua.3_Intron|GATS_uc010lgt.2_Intron|GATS_uc011kjl.1_Intron|GATS_uc010lgu.2_Intron|PVRIG_uc003uuf.1_Splice_Site_p.R199_splice	NM_024070	NP_076975			poliovirus receptor related immunoglobulin							integral to membrane				skin(2)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
PILRA	29992	broad.mit.edu	37	7	99971794	99971794	+	Silent	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99971794T>G	uc003uuo.1	+	2	404	c.192T>G	c.(190-192)GCT>GCG	p.A64A	PILRA_uc011kjn.1_Silent_p.A64A|PILRA_uc011kjo.1_Silent_p.A64A|PILRA_uc003uup.1_Silent_p.A64A|PILRA_uc003uuq.1_Silent_p.A64A	NM_013439	NP_038467	Q9UKJ1	PILRA_HUMAN	paired immunoglobulin-like type 2 receptor alpha	64	Extracellular (Potential).|Ig-like V-type.				interspecies interaction between organisms	extracellular region|integral to membrane|plasma membrane	protein binding|receptor activity			skin(1)	1	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	100550177	100550177	+	5'Flank	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100550177T>C	uc003uxk.1	+						uc003uxl.1_5'Flank					Homo sapiens MUC3B mRNA for intestinal mucin, partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	100551945	100551945	+	RNA	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100551945C>A	uc003uxk.1	+	1		c.1196C>A			uc003uxl.1_Silent_p.T132T					Homo sapiens MUC3B mRNA for intestinal mucin, partial cds.																														---	---	---	---
PLOD3	8985	broad.mit.edu	37	7	100855837	100855837	+	Silent	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100855837T>G	uc003uyd.2	-	9	1435	c.979A>C	c.(979-981)AGG>CGG	p.R327R	PLOD3_uc010lhs.2_5'UTR	NM_001084	NP_001075	O60568	PLOD3_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase	327					protein modification process	rough endoplasmic reticulum membrane	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-lysine 5-dioxygenase activity|protein binding			ovary(1)|skin(1)	2	Lung NSC(181;0.168)|all_lung(186;0.215)				Succinic acid(DB00139)|Vitamin C(DB00126)													---	---	---	---
SRPK2	6733	broad.mit.edu	37	7	104782775	104782775	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104782775T>A	uc003vct.2	-	10	1377	c.1190A>T	c.(1189-1191)CAA>CTA	p.Q397L	SRPK2_uc003vcu.2_Missense_Mutation_p.Q397L|SRPK2_uc003vcv.2_Missense_Mutation_p.Q408L|SRPK2_uc003vcw.1_Missense_Mutation_p.Q397L	NM_182691	NP_872633	P78362	SRPK2_HUMAN	serine/arginine-rich protein-specific kinase 2	397	Protein kinase.				angiogenesis|cell differentiation|intracellular protein kinase cascade|negative regulation of viral genome replication|nuclear speck organization|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of gene expression|positive regulation of neuron apoptosis|positive regulation of viral genome replication|spliceosome assembly	cytoplasm|nucleolus	14-3-3 protein binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity			central_nervous_system(3)|ovary(2)|upper_aerodigestive_tract(1)	6																		---	---	---	---
LAMB4	22798	broad.mit.edu	37	7	107706980	107706980	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107706980A>G	uc010ljo.1	-	20	2596	c.2512T>C	c.(2512-2514)TGC>CGC	p.C838R	LAMB4_uc003vey.2_Missense_Mutation_p.C838R|LAMB4_uc010ljp.1_5'Flank	NM_007356	NP_031382	A4D0S4	LAMB4_HUMAN	laminin, beta 4 precursor	838	Laminin EGF-like 7.				cell adhesion	basement membrane				ovary(4)|breast(2)|large_intestine(1)|skin(1)	8																		---	---	---	---
FOXP2	93986	broad.mit.edu	37	7	114298253	114298253	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114298253G>A	uc003vhb.2	+	11	1773	c.1399G>A	c.(1399-1401)GCC>ACC	p.A467T	FOXP2_uc003vgu.2_Intron|FOXP2_uc003vgz.2_Missense_Mutation_p.A492T|FOXP2_uc003vha.2_Missense_Mutation_p.A375T|FOXP2_uc011kmu.1_Missense_Mutation_p.A484T|FOXP2_uc011kmv.1_Missense_Mutation_p.A466T|FOXP2_uc010ljz.1_Intron|FOXP2_uc003vhe.1_Missense_Mutation_p.A37T	NM_014491	NP_055306	O15409	FOXP2_HUMAN	forkhead box P2 isoform I	467					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																		---	---	---	---
KCND2	3751	broad.mit.edu	37	7	120381662	120381662	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120381662T>C	uc003vjj.1	+	3	2318	c.1353T>C	c.(1351-1353)GGT>GGC	p.G451G		NM_012281	NP_036413	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related	451	Cytoplasmic (Potential).				regulation of action potential|synaptic transmission	cell surface|dendritic spine	metal ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5	all_neural(327;0.117)																	---	---	---	---
SLC13A1	6561	broad.mit.edu	37	7	122765664	122765664	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122765664G>T	uc003vkm.2	-	11	1224	c.1199C>A	c.(1198-1200)CCA>CAA	p.P400Q	SLC13A1_uc010lks.2_Missense_Mutation_p.P276Q	NM_022444	NP_071889	Q9BZW2	S13A1_HUMAN	solute carrier family 13 (sodium/sulfate	400	Helical; (Potential).					integral to membrane|plasma membrane	sodium:sulfate symporter activity			ovary(2)	2					Succinic acid(DB00139)													---	---	---	---
FSCN3	29999	broad.mit.edu	37	7	127235801	127235801	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127235801A>G	uc003vmd.1	+	2	804	c.585A>G	c.(583-585)ACA>ACG	p.T195T	FSCN3_uc003vmc.1_Silent_p.T150T|FSCN3_uc011kog.1_RNA|FSCN3_uc011koh.1_Silent_p.T61T|FSCN3_uc010llc.1_Silent_p.T195T	NM_020369	NP_065102	Q9NQT6	FSCN3_HUMAN	fascin 3	195						actin cytoskeleton|cytoplasm	actin filament binding|protein binding, bridging			ovary(1)	1																		---	---	---	---
RBM28	55131	broad.mit.edu	37	7	127961450	127961450	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127961450T>C	uc003vmp.2	-	14	1547	c.1432A>G	c.(1432-1434)AAG>GAG	p.K478E	RBM28_uc003vmo.2_Missense_Mutation_p.K95E|RBM28_uc011koj.1_Missense_Mutation_p.K337E	NM_018077	NP_060547	Q9NW13	RBM28_HUMAN	RNA binding motif protein 28	478					mRNA processing|RNA splicing	Golgi apparatus|nucleolus|spliceosomal complex	nucleotide binding|RNA binding			ovary(2)	2																		---	---	---	---
FLNC	2318	broad.mit.edu	37	7	128490504	128490504	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128490504A>G	uc003vnz.3	+	32	5574	c.5365A>G	c.(5365-5367)ATC>GTC	p.I1789V	FLNC_uc003voa.3_Missense_Mutation_p.I1756V	NM_001458	NP_001449	Q14315	FLNC_HUMAN	gamma filamin isoform a	1789	Filamin 16.				cell junction assembly	cytoskeleton|cytosol|plasma membrane|sarcomere	actin binding			breast(5)|large_intestine(3)|ovary(2)|central_nervous_system(1)|skin(1)	12																		---	---	---	---
FAM40B	57464	broad.mit.edu	37	7	129098126	129098126	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129098126C>T	uc011koy.1	+	10	1149	c.1109C>T	c.(1108-1110)GCC>GTC	p.A370V	FAM40B_uc003vow.2_Missense_Mutation_p.A370V|FAM40B_uc011koz.1_5'UTR	NM_020704	NP_065755	Q9ULQ0	FA40B_HUMAN	hypothetical protein LOC57464 isoform a	370											0																		---	---	---	---
CALD1	800	broad.mit.edu	37	7	134618140	134618140	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134618140A>G	uc003vrz.2	+	5	1079	c.620A>G	c.(619-621)CAG>CGG	p.Q207R	CALD1_uc003vry.2_Missense_Mutation_p.Q207R|CALD1_uc003vsa.2_Missense_Mutation_p.Q207R|CALD1_uc003vsb.2_Missense_Mutation_p.Q207R|CALD1_uc010lmm.2_Missense_Mutation_p.Q207R|CALD1_uc011kpt.1_5'UTR|CALD1_uc003vsc.2_Missense_Mutation_p.Q201R|CALD1_uc003vsd.2_Missense_Mutation_p.Q201R|CALD1_uc011kpu.1_Missense_Mutation_p.Q212R|CALD1_uc011kpv.1_Missense_Mutation_p.Q71R|CALD1_uc003vse.2_Missense_Mutation_p.Q71R	NM_033138	NP_149129	Q05682	CALD1_HUMAN	caldesmon 1 isoform 1	207	Myosin and calmodulin-binding (By similarity).				cellular component movement|muscle contraction	cytosol|focal adhesion|myofibril	actin binding|calmodulin binding|myosin binding|tropomyosin binding				0																		---	---	---	---
ADCK2	90956	broad.mit.edu	37	7	140373999	140373999	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140373999T>G	uc003vvy.1	+	1	1047	c.869T>G	c.(868-870)GTG>GGG	p.V290G	ADCK2_uc003vvz.2_Missense_Mutation_p.V290G	NM_052853	NP_443085	Q7Z695	ADCK2_HUMAN	aarF domain containing kinase 2	290	Protein kinase.					integral to membrane	ATP binding|protein serine/threonine kinase activity				0	Melanoma(164;0.00956)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	142428964	142428964	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142428964C>T	uc011krr.1	+						uc003vzp.2_Intron|uc011ksh.1_Intron|uc011ksi.1_Intron|uc003vzw.1_Intron|uc010loj.1_Intron|uc003wad.2_Intron|uc003wag.1_Silent_p.Y63Y|uc011ksg.1_Intron|uc011ksk.1_Silent_p.Y108Y					SubName: Full=V_segment translation product; Flags: Fragment;																														---	---	---	---
OR6V1	346517	broad.mit.edu	37	7	142749622	142749622	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142749622G>A	uc011ksv.1	+	1	185	c.185G>A	c.(184-186)GGC>GAC	p.G62D		NM_001001667	NP_001001667	Q8N148	OR6V1_HUMAN	olfactory receptor, family 6, subfamily V,	62	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	Melanoma(164;0.059)																	---	---	---	---
CLCN1	1180	broad.mit.edu	37	7	143047730	143047730	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143047730G>A	uc003wcr.1	+	22	2665	c.2578G>A	c.(2578-2580)GTC>ATC	p.V860I	CLCN1_uc011ktc.1_Missense_Mutation_p.V472I	NM_000083	NP_000074	P35523	CLCN1_HUMAN	chloride channel 1, skeletal muscle	860	CBS 2.|Cytoplasmic (By similarity).				muscle contraction	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5	Melanoma(164;0.205)																	---	---	---	---
ZNF746	155061	broad.mit.edu	37	7	149174007	149174007	+	Intron	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149174007C>A	uc003wfw.2	-						ZNF746_uc010lpi.2_Intron	NM_152557	NP_689770			zinc finger protein 746 isoform 2						negative regulation of transcription, DNA-dependent|neuron death|regulation of cell death|transcription, DNA-dependent	cytoplasm|nucleus	transcription regulatory region DNA binding|ubiquitin protein ligase binding|zinc ion binding			ovary(2)|breast(1)	3	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)															---	---	---	---
MLL3	58508	broad.mit.edu	37	7	151836298	151836298	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151836298T>C	uc003wla.2	-	57	14726	c.14507A>G	c.(14506-14508)GAC>GGC	p.D4836G	MLL3_uc003wkz.2_Missense_Mutation_p.D3950G|MLL3_uc003wkx.2_Missense_Mutation_p.D994G|MLL3_uc003wky.2_Missense_Mutation_p.D2396G	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	4836	SET.				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	151927079	151927079	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151927079C>A	uc003wla.2	-	18	3124	c.2905G>T	c.(2905-2907)GGA>TGA	p.G969*	MLL3_uc003wkz.2_Nonsense_Mutation_p.G30*	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	969	PHD-type 4.				intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)				N		medulloblastoma								---	---	---	---
ARHGEF10	9639	broad.mit.edu	37	8	1873486	1873486	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1873486C>T	uc003wpr.2	+	22	2704	c.2526C>T	c.(2524-2526)GAC>GAT	p.D842D	ARHGEF10_uc003wpq.1_Silent_p.D866D|ARHGEF10_uc003wps.2_Silent_p.D804D|ARHGEF10_uc003wpv.2_Silent_p.D574D|ARHGEF10_uc010lre.2_Silent_p.D522D	NM_014629	NP_055444	O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor 10	867					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)														---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	3224580	3224580	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3224580T>C	uc011kwk.1	-	20	3482	c.3092A>G	c.(3091-3093)TAC>TGC	p.Y1031C	CSMD1_uc011kwj.1_Missense_Mutation_p.Y423C|CSMD1_uc003wqe.2_Missense_Mutation_p.Y187C	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	1031	Extracellular (Potential).|CUB 6.					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)														---	---	---	---
SGK223	157285	broad.mit.edu	37	8	8185452	8185452	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8185452T>G	uc003wsh.3	-	4	2840	c.2840A>C	c.(2839-2841)GAG>GCG	p.E947A		NM_001080826	NP_001074295	Q86YV5	SG223_HUMAN	pragmin	947							ATP binding|non-membrane spanning protein tyrosine kinase activity				0																		---	---	---	---
MFHAS1	9258	broad.mit.edu	37	8	8748971	8748971	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8748971C>T	uc003wsj.1	-	1	2161	c.1598G>A	c.(1597-1599)TGC>TAC	p.C533Y		NM_004225	NP_004216	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified	533	Roc.										0		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)														---	---	---	---
USP17L2	377630	broad.mit.edu	37	8	11995032	11995032	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11995032G>T	uc003wvc.1	-	1	1238	c.1238C>A	c.(1237-1239)CCC>CAC	p.P413H	FAM66D_uc011kxp.1_Intron|FAM66D_uc011kxo.1_Intron	NM_201402	NP_958804	Q6R6M4	U17L2_HUMAN	deubiquitinating enzyme 3	413					apoptosis|cell cycle|G2/M transition checkpoint|mitotic cell cycle G1/S transition checkpoint|protein deubiquitination|ubiquitin-dependent protein catabolic process	nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			skin(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
MSR1	4481	broad.mit.edu	37	8	16012628	16012628	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16012628T>C	uc003wwz.2	-	6	1041	c.843A>G	c.(841-843)AAA>AAG	p.K281K	MSR1_uc010lsu.2_Silent_p.K299K|MSR1_uc003wxa.2_Silent_p.K281K|MSR1_uc003wxb.2_Silent_p.K281K|MSR1_uc011kxz.1_Silent_p.K55K	NM_138715	NP_619729	P21757	MSRE_HUMAN	macrophage scavenger receptor 1 isoform type 1	281	Collagen-like.|Extracellular (Potential).				cholesterol transport|plasma lipoprotein particle clearance|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis	collagen|integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|protein binding|scavenger receptor activity			ovary(1)	1				Colorectal(111;0.00475)|COAD - Colon adenocarcinoma(73;0.0164)														---	---	---	---
MTMR7	9108	broad.mit.edu	37	8	17206583	17206583	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17206583T>C	uc003wxm.2	-	5	715	c.476A>G	c.(475-477)GAC>GGC	p.D159G	MTMR7_uc003wxn.2_5'UTR	NM_004686	NP_004677	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7	159	Myotubularin phosphatase.						protein tyrosine phosphatase activity			skin(1)	1				Colorectal(111;0.112)														---	---	---	---
NAT2	10	broad.mit.edu	37	8	18257646	18257646	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18257646G>T	uc003wyw.1	+	2	240	c.133G>T	c.(133-135)GGG>TGG	p.G45W		NM_000015	NP_000006	P11245	ARY2_HUMAN	N-acetyltransferase 2	45					xenobiotic metabolic process	cytosol	arylamine N-acetyltransferase activity			ovary(1)|skin(1)	2				Colorectal(111;0.0531)|COAD - Colon adenocarcinoma(73;0.21)										Naso-/Oropharyngeal/Laryngeal_Cancer_Familial_Clustering_of				---	---	---	---
PSD3	23362	broad.mit.edu	37	8	18413798	18413798	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18413798C>T	uc003wza.2	-	15	2952	c.2849G>A	c.(2848-2850)CGC>CAC	p.R950H	PSD3_uc003wyx.3_Missense_Mutation_p.R279H|PSD3_uc003wyy.2_Missense_Mutation_p.R416H|PSD3_uc003wyz.2_Missense_Mutation_p.R251H	NM_015310	NP_056125	Q9NYI0	PSD3_HUMAN	ADP-ribosylation factor guanine nucleotide	951	Potential.				regulation of ARF protein signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	ARF guanyl-nucleotide exchange factor activity			ovary(3)	3				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)														---	---	---	---
ATP6V1B2	526	broad.mit.edu	37	8	20069218	20069218	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20069218T>C	uc003wzp.2	+	7	873	c.659T>C	c.(658-660)GTA>GCA	p.V220A		NM_001693	NP_001684	P21281	VATB2_HUMAN	vacuolar H+ATPase B2	220					ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|endomembrane system|Golgi apparatus|melanosome|plasma membrane|proton-transporting V-type ATPase, V1 domain	ATP binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism				0				Colorectal(74;0.0535)|COAD - Colon adenocarcinoma(73;0.211)														---	---	---	---
HR	55806	broad.mit.edu	37	8	21978727	21978727	+	Missense_Mutation	SNP	C	T	T	rs139027208		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21978727C>T	uc003xas.2	-	10	2883	c.2218G>A	c.(2218-2220)GCT>ACT	p.A740T	HR_uc003xat.2_Missense_Mutation_p.A740T	NM_005144	NP_005135	O43593	HAIR_HUMAN	hairless protein isoform a	740							DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|ovary(1)	2		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)														---	---	---	---
KIAA1967	57805	broad.mit.edu	37	8	22472984	22472984	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22472984C>T	uc003xch.2	+	12	1389	c.1252C>T	c.(1252-1254)CGG>TGG	p.R418W	KIAA1967_uc003xci.2_Missense_Mutation_p.R418W|KIAA1967_uc003xcj.1_Missense_Mutation_p.R87W	NM_199205	NP_954675	Q8N163	K1967_HUMAN	p30 DBC protein	418					apoptosis|positive regulation of apoptosis	mitochondrial matrix|nucleus	enzyme binding|enzyme inhibitor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00593)|Colorectal(74;0.0157)|COAD - Colon adenocarcinoma(73;0.064)														---	---	---	---
LOXL2	4017	broad.mit.edu	37	8	23225532	23225532	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23225532G>A	uc003xdh.1	-	2	672	c.333C>T	c.(331-333)AGC>AGT	p.S111S		NM_002318	NP_002309	Q9Y4K0	LOXL2_HUMAN	lysyl oxidase-like 2 precursor	111	SRCR 1.				aging|cell adhesion|protein modification process	extracellular space|membrane	copper ion binding|electron carrier activity|oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor|scavenger receptor activity			breast(2)|ovary(1)	3		Prostate(55;0.0453)|Breast(100;0.143)		Colorectal(74;0.0288)|COAD - Colon adenocarcinoma(73;0.096)														---	---	---	---
NKX3-1	4824	broad.mit.edu	37	8	23538765	23538765	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23538765C>T	uc011kzx.1	-	2	722	c.674G>A	c.(673-675)TGC>TAC	p.C225Y	NKX3-1_uc003xdv.1_Intron	NM_006167	NP_006158	Q99801	NKX31_HUMAN	NK3 homeobox 1	225					negative regulation of estrogen receptor binding|negative regulation of transcription, DNA-dependent|positive regulation of cell division|positive regulation of mitotic cell cycle|positive regulation of transcription from RNA polymerase II promoter	nucleus	estrogen receptor activity|estrogen receptor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region sequence-specific DNA binding				0		Prostate(55;0.114)		Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)|BRCA - Breast invasive adenocarcinoma(99;0.0708)														---	---	---	---
NEFM	4741	broad.mit.edu	37	8	24772078	24772078	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24772078C>T	uc003xed.3	+	1	805	c.772C>T	c.(772-774)CGC>TGC	p.R258C	NEFM_uc011lac.1_Missense_Mutation_p.R258C|NEFM_uc010lue.2_5'Flank|uc010luc.1_5'UTR	NM_005382	NP_005373	P07197	NFM_HUMAN	neurofilament, medium polypeptide 150kDa isoform	258	Linker 12.|Rod.					neurofilament	protein binding|structural constituent of cytoskeleton			breast(1)	1		Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)														---	---	---	---
TRIM35	23087	broad.mit.edu	37	8	27145435	27145435	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27145435C>T	uc003xfl.1	-	6	1196	c.1114G>A	c.(1114-1116)GTG>ATG	p.V372M	TRIM35_uc010lup.1_3'UTR	NM_171982	NP_741983	Q9UPQ4	TRI35_HUMAN	tripartite motif-containing 35 isoform 2	372	B30.2/SPRY.				apoptosis|induction of apoptosis|negative regulation of mitotic cell cycle	cytoplasm|nucleus	zinc ion binding				0		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0213)|Epithelial(17;9.34e-10)|Colorectal(74;0.141)														---	---	---	---
NRG1	3084	broad.mit.edu	37	8	32617872	32617872	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32617872A>G	uc003xiv.2	+	11	1733	c.1216A>G	c.(1216-1218)AGG>GGG	p.R406G	NRG1_uc011lbf.1_Missense_Mutation_p.R403G|NRG1_uc010lvo.2_Missense_Mutation_p.R403G|NRG1_uc003xiu.2_Missense_Mutation_p.R411G|NRG1_uc003xiw.2_Missense_Mutation_p.R403G|NRG1_uc003xit.2_Missense_Mutation_p.R406G|NRG1_uc010lvr.2_Missense_Mutation_p.R148G|NRG1_uc010lvs.2_Missense_Mutation_p.R148G|NRG1_uc010lvp.2_Missense_Mutation_p.R360G|NRG1_uc010lvq.2_Missense_Mutation_p.R343G|NRG1_uc011lbg.1_Missense_Mutation_p.R252G|NRG1_uc011lbh.1_Missense_Mutation_p.R249G|NRG1_uc003xja.2_Missense_Mutation_p.R217G	NM_013964	NP_039258	Q02297	NRG1_HUMAN	neuregulin 1 isoform HRG-alpha	406	Cytoplasmic (Potential).				activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)														---	---	---	---
NRG1	3084	broad.mit.edu	37	8	32621376	32621376	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32621376C>T	uc003xiv.2	+	12	1896	c.1379C>T	c.(1378-1380)ACG>ATG	p.T460M	NRG1_uc010lvo.2_3'UTR|NRG1_uc003xiu.2_Missense_Mutation_p.T465M|NRG1_uc003xiw.2_Missense_Mutation_p.T457M|NRG1_uc003xit.2_3'UTR|NRG1_uc010lvr.2_Missense_Mutation_p.T202M|NRG1_uc010lvs.2_Missense_Mutation_p.T202M|NRG1_uc010lvp.2_Missense_Mutation_p.T414M|NRG1_uc010lvq.2_Missense_Mutation_p.T397M|NRG1_uc011lbg.1_3'UTR|NRG1_uc011lbh.1_Missense_Mutation_p.T303M|NRG1_uc003xja.2_Missense_Mutation_p.T271M	NM_013964	NP_039258	Q02297	NRG1_HUMAN	neuregulin 1 isoform HRG-alpha	460	Cytoplasmic (Potential).				activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)														---	---	---	---
WHSC1L1	54904	broad.mit.edu	37	8	38157109	38157109	+	Splice_Site	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38157109C>A	uc003xli.2	-	15	3130	c.2612_splice	c.e15-1	p.G871_splice	WHSC1L1_uc011lbm.1_Splice_Site_p.G871_splice|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								---	---	---	---
IDO1	3620	broad.mit.edu	37	8	39782291	39782291	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39782291G>T	uc003xnm.2	+	8	821	c.707G>T	c.(706-708)GGC>GTC	p.G236V	IDO1_uc003xnn.2_RNA	NM_002164	NP_002155	P14902	I23O1_HUMAN	indoleamine 2,3-dioxygenase 1	236					female pregnancy|tryptophan catabolic process	cytosol	electron carrier activity|heme binding|indoleamine 2,3-dioxygenase activity|tryptophan 2,3-dioxygenase activity			central_nervous_system(2)	2					L-Tryptophan(DB00150)													---	---	---	---
CHRNA6	8973	broad.mit.edu	37	8	42620259	42620259	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42620259G>A	uc003xpj.2	-	2	214	c.168C>T	c.(166-168)TCC>TCT	p.S56S	CHRNA6_uc011lcw.1_Silent_p.S56S	NM_004198	NP_004189	Q15825	ACHA6_HUMAN	cholinergic receptor, nicotinic, alpha 6	56	Extracellular.					cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity				0	all_lung(13;3.33e-12)|Lung NSC(13;9.17e-11)|Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00439)|Lung NSC(58;0.0124)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	Lung(22;0.0252)|LUSC - Lung squamous cell carcinoma(45;0.0869)															---	---	---	---
PXDNL	137902	broad.mit.edu	37	8	52321627	52321627	+	Silent	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52321627G>T	uc003xqu.3	-	17	2658	c.2557C>A	c.(2557-2559)CGG>AGG	p.R853R	PXDNL_uc003xqt.3_RNA	NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like precursor	853					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	52370198	52370198	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52370198C>A	uc003xqu.3	-	9	943	c.842G>T	c.(841-843)CGA>CTA	p.R281L		NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like precursor	281	Ig-like C2-type 1.				hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)																---	---	---	---
PCMTD1	115294	broad.mit.edu	37	8	52733197	52733197	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52733197A>T	uc003xqx.3	-	6	1129	c.788T>A	c.(787-789)ATG>AAG	p.M263K	PCMTD1_uc011ldm.1_Missense_Mutation_p.M133K|PCMTD1_uc003xqw.3_Missense_Mutation_p.M263K|PCMTD1_uc011ldn.1_Missense_Mutation_p.M75K|PCMTD1_uc010lya.2_Missense_Mutation_p.M187K	NM_052937	NP_443169	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate)	263						cytoplasm	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity				0		Lung NSC(129;0.0795)|all_lung(136;0.144)																---	---	---	---
XKR4	114786	broad.mit.edu	37	8	56270442	56270442	+	Intron	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56270442G>T	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)															---	---	---	---
PLAG1	5324	broad.mit.edu	37	8	57079964	57079964	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57079964T>G	uc003xsq.3	-	3	792	c.341A>C	c.(340-342)CAC>CCC	p.H114P	PLAG1_uc003xsr.3_Missense_Mutation_p.H114P|PLAG1_uc010lyi.2_Missense_Mutation_p.H114P|PLAG1_uc010lyj.2_Missense_Mutation_p.H32P	NM_001114635	NP_001108107	Q6DJT9	PLAG1_HUMAN	pleiomorphic adenoma gene 1 isoform b	114	Decreased nuclear import with localization in the nucleus but also in the cytoplasm.|C2H2-type 3.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding		CTNNB1/PLAG1(60)|FGFR1_ENST00000447712/PLAG1(28)|CHCHD7/PLAG1(12)|LIFR_ENST00000263409/PLAG1(10)|HAS2/PLAG1(10)|COL1A2/PLAG1(3)|TCEA1_ENST00000521604/PLAG1(3)	salivary_gland(113)|soft_tissue(13)|lung(1)|central_nervous_system(1)|breast(1)	129		all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.125)	Epithelial(17;0.00179)|all cancers(17;0.0125)					T	TCEA1|LIFR|CTNNB1|CHCHD7	salivary adenoma								---	---	---	---
CHD7	55636	broad.mit.edu	37	8	61654649	61654649	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61654649C>A	uc003xue.2	+	2	1135	c.658C>A	c.(658-660)CTC>ATC	p.L220I		NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	220	Gln-rich.				central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity			ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)															---	---	---	---
CHD7	55636	broad.mit.edu	37	8	61713081	61713081	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61713081G>T	uc003xue.2	+	5	2850	c.2373G>T	c.(2371-2373)CAG>CAT	p.Q791H		NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	791					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	61769233	61769233	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61769233T>G	uc003xue.2	+	34	7871	c.7394T>G	c.(7393-7395)TTT>TGT	p.F2465C		NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2465					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)															---	---	---	---
PDE7A	5150	broad.mit.edu	37	8	66695013	66695013	+	Intron	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66695013C>A	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)													---	---	---	---
PREX2	80243	broad.mit.edu	37	8	68984801	68984801	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68984801C>T	uc003xxv.1	+	14	1592	c.1565C>T	c.(1564-1566)GCA>GTA	p.A522V	PREX2_uc003xxu.1_Missense_Mutation_p.A522V|PREX2_uc011lez.1_Missense_Mutation_p.A457V	NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a	522	DEP 2.				G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17																		---	---	---	---
CA1	759	broad.mit.edu	37	8	86245775	86245775	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86245775T>C	uc003ydh.2	-	6	629	c.429A>G	c.(427-429)GCA>GCG	p.A143A	CA13_uc003ydf.1_Intron|CA1_uc010mae.1_Silent_p.A143A|CA1_uc003ydi.2_Silent_p.A143A	NM_001738	NP_001729	P00915	CAH1_HUMAN	carbonic anhydrase I	143					one-carbon metabolic process	Golgi apparatus	carbonate dehydratase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2		all_lung(136;4.89e-06)			Acetazolamide(DB00819)|Amlodipine(DB00381)|Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Brinzolamide(DB01194)|Chlorothiazide(DB00880)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Dichlorphenamide(DB01144)|Ethinamate(DB01031)|Ethoxzolamide(DB00311)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Levetiracetam(DB01202)|Methazolamide(DB00703)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)|Verapamil(DB00661)|Zonisamide(DB00909)													---	---	---	---
CNBD1	168975	broad.mit.edu	37	8	88365904	88365904	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88365904A>G	uc003ydy.2	+	10	1241	c.1193A>G	c.(1192-1194)GAG>GGG	p.E398G		NM_173538	NP_775809	Q8NA66	CNBD1_HUMAN	cyclic nucleotide binding domain containing 1	398	cNMP.									ovary(3)	3																		---	---	---	---
PLEKHF2	79666	broad.mit.edu	37	8	96166551	96166551	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96166551G>T	uc003yhn.1	+	2	526	c.279G>T	c.(277-279)GAG>GAT	p.E93D		NM_024613	NP_078889	Q9H8W4	PKHF2_HUMAN	phafin 2	93	PH.					transport vesicle	metal ion binding|protein binding			ovary(2)	2	Breast(36;3.18e-05)																	---	---	---	---
POP1	10940	broad.mit.edu	37	8	99168419	99168419	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99168419T>C	uc003yij.3	+	15	2299	c.2199T>C	c.(2197-2199)GGT>GGC	p.G733G	POP1_uc011lgv.1_Silent_p.G733G|POP1_uc003yik.2_Silent_p.G733G	NM_001145860	NP_001139332	Q99575	POP1_HUMAN	processing of precursor 1	733					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)															---	---	---	---
MIR875	100126309	broad.mit.edu	37	8	100549062	100549062	+	RNA	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100549062T>C	hsa-mir-875|MI0005541	-			c.28T>C			VPS13B_uc003yiv.2_Intron|VPS13B_uc003yiw.2_Intron|MIR599_hsa-mir-599|MI0003611_5'Flank																	0																		---	---	---	---
UBR5	51366	broad.mit.edu	37	8	103307428	103307428	+	Intron	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103307428G>A	uc003ykr.1	-						UBR5_uc003yks.1_Intron	NM_015902	NP_056986			ubiquitin protein ligase E3 component n-recognin						cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	28	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)															---	---	---	---
UBR5	51366	broad.mit.edu	37	8	103311746	103311746	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103311746C>T	uc003ykr.1	-	24	3169	c.3136G>A	c.(3136-3138)GCT>ACT	p.A1046T	UBR5_uc003yks.1_Missense_Mutation_p.A1046T	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin	1046					cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	28	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)															---	---	---	---
BAALC	79870	broad.mit.edu	37	8	104225229	104225229	+	Silent	SNP	G	A	A	rs138529581	byFrequency	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104225229G>A	uc003yld.2	+	2	448	c.243G>A	c.(241-243)ACG>ACA	p.T81T	BAALC_uc003yle.2_Intron|uc003ylf.2_Intron|BAALC_uc003ylg.2_Silent_p.T27T|BAALC_uc010mcc.2_5'Flank	NM_024812	NP_079088	Q8WXS3	BAALC_HUMAN	brain and acute leukemia, cytoplasmic isoform 1	116						centrosome|membrane|nucleus					0			OV - Ovarian serous cystadenocarcinoma(57;3.49e-05)|STAD - Stomach adenocarcinoma(118;0.133)															---	---	---	---
CTHRC1	115908	broad.mit.edu	37	8	104388009	104388009	+	Missense_Mutation	SNP	G	A	A	rs147175675	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104388009G>A	uc003ylk.2	+	2	293	c.194G>A	c.(193-195)CGA>CAA	p.R65Q	CTHRC1_uc011lhq.1_Missense_Mutation_p.R65Q	NM_138455	NP_612464	Q96CG8	CTHR1_HUMAN	collagen triple helix repeat containing 1	65	Collagen-like.					collagen				ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)															---	---	---	---
RIMS2	9699	broad.mit.edu	37	8	104955062	104955062	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104955062C>T	uc003yls.2	+	12	2184	c.1943C>T	c.(1942-1944)ACG>ATG	p.T648M	RIMS2_uc003ylp.2_Missense_Mutation_p.T870M|RIMS2_uc003ylw.2_Missense_Mutation_p.T662M|RIMS2_uc003ylq.2_Missense_Mutation_p.T662M|RIMS2_uc003ylr.2_Missense_Mutation_p.T709M|RIMS2_uc003ylt.2_Missense_Mutation_p.T255M	NM_014677	NP_055492	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	932					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)			---	---	---	---
TM7SF4	81501	broad.mit.edu	37	8	105361366	105361366	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105361366G>A	uc003ylx.1	+	2	635	c.586G>A	c.(586-588)GTC>ATC	p.V196I		NM_030788	NP_110415	Q9H295	TM7S4_HUMAN	dendritic cell-specific transmembrane protein	196					osteoclast differentiation	cell surface|integral to membrane|plasma membrane				pancreas(2)|large_intestine(1)|ovary(1)	4			OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)															---	---	---	---
ANGPT1	284	broad.mit.edu	37	8	108359208	108359208	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108359208C>T	uc003ymn.2	-	2	883	c.415G>A	c.(415-417)GCA>ACA	p.A139T	ANGPT1_uc003ymo.2_Missense_Mutation_p.A139T	NM_001146	NP_001137	Q15389	ANGP1_HUMAN	angiopoietin 1 precursor	139					activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|blood coagulation|cell differentiation|heparin biosynthetic process|leukocyte migration|negative regulation of cell adhesion|negative regulation of endothelial cell apoptosis|negative regulation of vascular permeability|positive chemotaxis|positive regulation of blood vessel endothelial cell migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of protein ubiquitination|positive regulation of receptor internalization|protein localization at cell surface|regulation of satellite cell proliferation|sprouting angiogenesis|Tie receptor signaling pathway	extracellular space|membrane raft|microvillus|plasma membrane	receptor tyrosine kinase binding			ovary(3)|skin(3)|upper_aerodigestive_tract(1)	7	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)															---	---	---	---
RSPO2	340419	broad.mit.edu	37	8	109001376	109001376	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109001376C>T	uc003yms.2	-	3	849	c.191G>A	c.(190-192)CGA>CAA	p.R64Q	RSPO2_uc003ymq.2_5'UTR|RSPO2_uc003ymr.2_Intron	NM_178565	NP_848660	Q6UXX9	RSPO2_HUMAN	R-spondin family, member 2 precursor	64					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)															---	---	---	---
PKHD1L1	93035	broad.mit.edu	37	8	110412581	110412581	+	Intron	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110412581A>G	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)			---	---	---	---
PKHD1L1	93035	broad.mit.edu	37	8	110432903	110432903	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110432903C>T	uc003yne.2	+	23	2785	c.2681C>T	c.(2680-2682)GCT>GTT	p.A894V		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	894	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	113694841	113694841	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113694841T>A	uc003ynu.2	-	16	2666	c.2507A>T	c.(2506-2508)GAT>GTT	p.D836V	CSMD3_uc003yns.2_Missense_Mutation_p.D108V|CSMD3_uc003ynt.2_Missense_Mutation_p.D796V|CSMD3_uc011lhx.1_Missense_Mutation_p.D732V	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	836	Sushi 4.|Extracellular (Potential).					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	114111188	114111188	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114111188T>G	uc003ynu.2	-	5	873	c.714A>C	c.(712-714)GAA>GAC	p.E238D	CSMD3_uc003ynt.2_Missense_Mutation_p.E198D|CSMD3_uc011lhx.1_Missense_Mutation_p.E238D|CSMD3_uc010mcx.1_Missense_Mutation_p.E238D	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	238	Extracellular (Potential).					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
COL14A1	7373	broad.mit.edu	37	8	121326207	121326207	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121326207G>T	uc003yox.2	+	38	4757	c.4492G>T	c.(4492-4494)GGA>TGA	p.G1498*	COL14A1_uc003yoz.2_Nonsense_Mutation_p.G463*	NM_021110	NP_066933	Q05707	COEA1_HUMAN	collagen, type XIV, alpha 1 precursor	1498	Triple-helical region 1 (COL2).				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)															---	---	---	---
KLHL38	340359	broad.mit.edu	37	8	124664715	124664715	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124664715A>G	uc003yqs.1	-	1	476	c.452T>C	c.(451-453)CTC>CCC	p.L151P		NM_001081675	NP_001075144	Q2WGJ6	KLH38_HUMAN	kelch-like 38	151	BACK.										0																		---	---	---	---
FER1L6	654463	broad.mit.edu	37	8	124985729	124985729	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124985729T>C	uc003yqw.2	+	7	709	c.503T>C	c.(502-504)CTG>CCG	p.L168P		NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6	168	Cytoplasmic (Potential).					integral to membrane				ovary(5)|skin(5)|central_nervous_system(1)	11	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)															---	---	---	---
RNF139	11236	broad.mit.edu	37	8	125498088	125498088	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125498088T>C	uc003yrc.2	+	2	541	c.198T>C	c.(196-198)AGT>AGC	p.S66S		NM_007218	NP_009149	Q8WU17	RN139_HUMAN	ring finger protein 139	66	Helical; (Potential).				negative regulation of cell proliferation|regulation of protein ubiquitination	endoplasmic reticulum membrane|integral to membrane	protein binding|receptor activity|ubiquitin-protein ligase activity|zinc ion binding			kidney(1)	1	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)											Renal_Cell_Cancer_associated_with_constitutional_translocation_of_chromosome_3				---	---	---	---
ZNF572	137209	broad.mit.edu	37	8	125988852	125988852	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125988852A>G	uc003yrr.2	+	3	497	c.342A>G	c.(340-342)GGA>GGG	p.G114G		NM_152412	NP_689625	Q7Z3I7	ZN572_HUMAN	zinc finger protein 572	114					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)												HNSCC(60;0.17)			---	---	---	---
KIAA0196	9897	broad.mit.edu	37	8	126056120	126056120	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126056120C>T	uc003yrt.2	-	23	3126	c.2797G>A	c.(2797-2799)GCC>ACC	p.A933T	KIAA0196_uc011lir.1_Missense_Mutation_p.A785T|KIAA0196_uc003yru.1_Missense_Mutation_p.A507T	NM_014846	NP_055661	Q12768	STRUM_HUMAN	strumpellin	933					cell death	WASH complex				ovary(2)	2	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)															---	---	---	---
KCNQ3	3786	broad.mit.edu	37	8	133192417	133192417	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133192417C>T	uc003ytj.2	-	4	989	c.764G>A	c.(763-765)TGT>TAT	p.C255Y	KCNQ3_uc010mdt.2_Missense_Mutation_p.C255Y	NM_004519	NP_004510	O43525	KCNQ3_HUMAN	potassium voltage-gated channel KQT-like protein	255					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)															---	---	---	---
COL22A1	169044	broad.mit.edu	37	8	139791774	139791774	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139791774A>G	uc003yvd.2	-	14	2129	c.1682T>C	c.(1681-1683)CTG>CCG	p.L561P		NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	561	Pro-rich.|Gly-rich.|Collagen-like 2.				cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)												HNSCC(7;0.00092)			---	---	---	---
EIF2C2	27161	broad.mit.edu	37	8	141595330	141595330	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141595330C>A	uc003yvn.2	-	2	143	c.103G>T	c.(103-105)GGG>TGG	p.G35W	EIF2C2_uc010men.2_Intron|EIF2C2_uc010meo.2_Missense_Mutation_p.G35W	NM_012154	NP_036286	Q9UKV8	AGO2_HUMAN	argonaute 2 isoform 1	35					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)															---	---	---	---
TSNARE1	203062	broad.mit.edu	37	8	143427122	143427122	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143427122G>T	uc003ywk.2	-	3	338	c.220C>A	c.(220-222)CCA>ACA	p.P74T	TSNARE1_uc011lju.1_Missense_Mutation_p.P74T|TSNARE1_uc003ywj.2_Missense_Mutation_p.P74T|TSNARE1_uc003ywl.3_Intron	NM_145003	NP_659440	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	74					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)																	---	---	---	---
PYCRL	65263	broad.mit.edu	37	8	144687973	144687973	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144687973G>A	uc003yyy.2	-	6	768	c.758C>T	c.(757-759)ACC>ATC	p.T253I	PYCRL_uc011lkm.1_Missense_Mutation_p.T233I|PYCRL_uc011lkn.1_RNA	NM_023078	NP_075566	Q53H96	P5CR3_HUMAN	pyrroline-5-carboxylate reductase-like	241					proline biosynthetic process		pyrroline-5-carboxylate reductase activity				0	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.17e-38)|Epithelial(56;7.17e-37)|all cancers(56;2.46e-32)|Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)															---	---	---	---
FAM83H	286077	broad.mit.edu	37	8	144811126	144811126	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144811126C>T	uc003yzk.2	-						FAM83H_uc010mfk.1_5'Flank	NM_198488	NP_940890			FAM83H						biomineral tissue development					lung(1)|central_nervous_system(1)|pancreas(1)	3	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)															---	---	---	---
EPPK1	83481	broad.mit.edu	37	8	144942019	144942019	+	Silent	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144942019G>T	uc003zaa.1	-	1	5416	c.5403C>A	c.(5401-5403)TCC>TCA	p.S1801S		NM_031308	NP_112598	P58107	EPIPL_HUMAN	epiplakin 1	1801						cytoplasm|cytoskeleton	protein binding|structural molecule activity			pancreas(1)|skin(1)	2	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)															---	---	---	---
PLEC	5339	broad.mit.edu	37	8	144994831	144994831	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144994831A>G	uc003zaf.1	-	32	9739	c.9569T>C	c.(9568-9570)ATG>ACG	p.M3190T	PLEC_uc003zab.1_Missense_Mutation_p.M3053T|PLEC_uc003zac.1_Missense_Mutation_p.M3057T|PLEC_uc003zad.2_Missense_Mutation_p.M3053T|PLEC_uc003zae.1_Missense_Mutation_p.M3021T|PLEC_uc003zag.1_Missense_Mutation_p.M3031T|PLEC_uc003zah.2_Missense_Mutation_p.M3039T|PLEC_uc003zaj.2_Missense_Mutation_p.M3080T	NM_201380	NP_958782	Q15149	PLEC_HUMAN	plectin isoform 1	3190	Globular 2.|Plectin 7.				cellular component disassembly involved in apoptosis|hemidesmosome assembly	cytosol|focal adhesion|hemidesmosome|intermediate filament cytoskeleton|sarcolemma	actin binding|structural constituent of muscle|structural constituent of muscle			large_intestine(2)|ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	9																		---	---	---	---
PLEC	5339	broad.mit.edu	37	8	145012854	145012854	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145012854C>A	uc003zaf.1	-	2	700	c.530G>T	c.(529-531)CGG>CTG	p.R177L	PLEC_uc003zab.1_Missense_Mutation_p.R40L|PLEC_uc003zac.1_Missense_Mutation_p.R44L|PLEC_uc003zad.2_Missense_Mutation_p.R40L|PLEC_uc003zae.1_Missense_Mutation_p.R8L|PLEC_uc003zag.1_Missense_Mutation_p.R18L|PLEC_uc003zah.2_Missense_Mutation_p.R26L|PLEC_uc003zaj.2_Missense_Mutation_p.R67L	NM_201380	NP_958782	Q15149	PLEC_HUMAN	plectin isoform 1	177	Globular 1.|Actin-binding.				cellular component disassembly involved in apoptosis|hemidesmosome assembly	cytosol|focal adhesion|hemidesmosome|intermediate filament cytoskeleton|sarcolemma	actin binding|structural constituent of muscle|structural constituent of muscle			large_intestine(2)|ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	9																		---	---	---	---
PLEC	5339	broad.mit.edu	37	8	145013538	145013538	+	Intron	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145013538C>A	uc003zaf.1	-						PLEC_uc003zab.1_Missense_Mutation_p.R31M|PLEC_uc003zac.1_Intron|PLEC_uc003zad.2_Intron|PLEC_uc003zae.1_Intron|PLEC_uc003zag.1_Intron|PLEC_uc003zah.2_Intron|PLEC_uc003zaj.2_Intron	NM_201380	NP_958782			plectin isoform 1						cellular component disassembly involved in apoptosis|hemidesmosome assembly	cytosol|focal adhesion|hemidesmosome|intermediate filament cytoskeleton|sarcolemma	actin binding|structural constituent of muscle|structural constituent of muscle			large_intestine(2)|ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	9																		---	---	---	---
PARP10	84875	broad.mit.edu	37	8	145058828	145058828	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145058828G>A	uc003zal.3	-	5	1450	c.1342C>T	c.(1342-1344)CTA>TTA	p.L448L	PARP10_uc003zak.3_Silent_p.L154L|PARP10_uc011lku.1_Silent_p.L460L|PARP10_uc011lkv.1_RNA|PARP10_uc003zam.2_Silent_p.L448L|PARP10_uc010mfn.1_Silent_p.L363L|PARP10_uc010mfo.1_3'UTR	NM_032789	NP_116178	Q53GL7	PAR10_HUMAN	poly (ADP-ribose) polymerase family, member 10	448						Golgi apparatus|nucleolus	NAD+ ADP-ribosyltransferase activity|nucleotide binding			ovary(2)|upper_aerodigestive_tract(1)|lung(1)|breast(1)|pancreas(1)	6	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)															---	---	---	---
MGC70857	414919	broad.mit.edu	37	8	145753401	145753401	+	Intron	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145753401G>T	uc003zdp.1	-						LRRC24_uc003zdm.2_5'Flank|LRRC24_uc003zdn.2_5'Flank|MGC70857_uc003zdq.1_Translation_Start_Site|MGC70857_uc003zdr.1_Intron	NM_001001795	NP_001001795			hypothetical protein LOC414919												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)															---	---	---	---
DMRT3	58524	broad.mit.edu	37	9	990270	990270	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:990270T>C	uc003zgw.1	+	2	722	c.684T>C	c.(682-684)AAT>AAC	p.N228N		NM_021240	NP_067063	Q9NQL9	DMRT3_HUMAN	doublesex and mab-3 related transcription factor	228					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)														---	---	---	---
GLIS3	169792	broad.mit.edu	37	9	4118573	4118573	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4118573G>A	uc003zhw.1	-	3	634	c.440C>T	c.(439-441)GCG>GTG	p.A147V	GLIS3_uc003zhx.1_Missense_Mutation_p.A302V|GLIS3_uc003zic.1_Missense_Mutation_p.A302V|GLIS3_uc003zie.1_Missense_Mutation_p.A302V|GLIS3_uc010mhh.1_Missense_Mutation_p.A177V|GLIS3_uc003zid.1_Missense_Mutation_p.A80V|GLIS3_uc010mhi.1_Missense_Mutation_p.A109V|GLIS3_uc003zif.1_Missense_Mutation_p.A80V|GLIS3_uc003zig.1_Missense_Mutation_p.A146V|GLIS3_uc003zih.1_Missense_Mutation_p.A80V|GLIS3_uc003zhy.1_Missense_Mutation_p.A80V|GLIS3_uc003zhz.1_Missense_Mutation_p.A80V|GLIS3_uc003zib.1_Missense_Mutation_p.A146V|GLIS3_uc010mhg.1_Missense_Mutation_p.A80V	NM_152629	NP_689842	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3 isoform b	147	Ser-rich.				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)														---	---	---	---
KDM4C	23081	broad.mit.edu	37	9	7046853	7046853	+	Intron	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7046853T>C	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																		---	---	---	---
FAM154A	158297	broad.mit.edu	37	9	18928655	18928655	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18928655A>C	uc003zni.1	-	4	1098	c.820T>G	c.(820-822)TTT>GTT	p.F274V	FAM154A_uc010mip.1_Missense_Mutation_p.F82V	NM_153707	NP_714918	Q8IYX7	F154A_HUMAN	hypothetical protein LOC158297	274										pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.53e-16)														---	---	---	---
ACER2	340485	broad.mit.edu	37	9	19450617	19450617	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19450617T>G	uc003zny.1	+	6	969	c.811T>G	c.(811-813)TCA>GCA	p.S271A	ACER2_uc003znx.1_RNA|ACER2_uc003znz.1_Missense_Mutation_p.S222A	NM_001010887	NP_001010887	Q5QJU3	ACER2_HUMAN	alkaline ceramidase 2	271	Cytoplasmic (Potential).				ceramide metabolic process|negative regulation of cell adhesion mediated by integrin|negative regulation of cell-matrix adhesion|negative regulation of protein glycosylation in Golgi|positive regulation of cell proliferation|response to retinoic acid|sphingosine biosynthetic process	integral to Golgi membrane	ceramidase activity			haematopoietic_and_lymphoid_tissue(1)|skin(1)	2																		---	---	---	---
TEK	7010	broad.mit.edu	37	9	27183486	27183486	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27183486G>A	uc003zqi.3	+	8	1502	c.1060G>A	c.(1060-1062)GAT>AAT	p.D354N	TEK_uc011lnn.1_Missense_Mutation_p.G357E|TEK_uc011lno.1_Missense_Mutation_p.D311N|TEK_uc011lnp.1_Missense_Mutation_p.D207N|TEK_uc003zqj.1_Missense_Mutation_p.D288N	NM_000459	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial precursor	354	Extracellular (Potential).|Ig-like C2-type 2.				angiogenesis|blood coagulation|cell-cell signaling|leukocyte migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein kinase B signaling cascade|protein oligomerization|transmembrane receptor protein tyrosine kinase signaling pathway	apical plasma membrane|basolateral plasma membrane|cell surface|integral to plasma membrane|membrane raft|microvillus	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity			ovary(3)|central_nervous_system(3)|breast(3)|lung(2)|kidney(1)	12		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)														---	---	---	---
TOPORS	10210	broad.mit.edu	37	9	32542121	32542121	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32542121C>T	uc003zrb.2	-	3	2569	c.2402G>A	c.(2401-2403)CGG>CAG	p.R801Q	TOPORS_uc003zrc.2_Missense_Mutation_p.R734Q	NM_005802	NP_005793	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich	801	Interaction with TOP1.				DNA damage response, signal transduction resulting in induction of apoptosis|maintenance of protein location in nucleus|proteasomal ubiquitin-dependent protein catabolic process|protein sumoylation|transcription, DNA-dependent	nuclear speck|PML body	antigen binding|DNA binding|DNA topoisomerase I binding|SUMO ligase activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)														---	---	---	---
TAF1L	138474	broad.mit.edu	37	9	32634799	32634799	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32634799C>T	uc003zrg.1	-	1	869	c.779G>A	c.(778-780)CGC>CAC	p.R260H	uc003zrh.1_RNA	NM_153809	NP_722516	Q8IZX4	TAF1L_HUMAN	TBP-associated factor RNA polymerase 1-like	260					male meiosis|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	transcription factor TFIID complex	DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding			lung(8)|skin(6)|central_nervous_system(4)|large_intestine(3)|ovary(2)|stomach(1)|breast(1)|pancreas(1)	26			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)														---	---	---	---
NFX1	4799	broad.mit.edu	37	9	33352697	33352697	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33352697A>C	uc003zsq.2	+	17	2770	c.2709A>C	c.(2707-2709)GAA>GAC	p.E903D	SUGT1P1_uc010mjq.1_Intron|NFX1_uc003zsp.1_Missense_Mutation_p.E903D|NFX1_uc010mjr.1_Missense_Mutation_p.E904D|NFX1_uc003zsr.2_Missense_Mutation_p.E904D	NM_002504	NP_002495	Q12986	NFX1_HUMAN	nuclear transcription factor, X-box binding 1	903					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)														---	---	---	---
UBAP1	51271	broad.mit.edu	37	9	34241797	34241797	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34241797T>C	uc003ztx.2	+	4	1009	c.774T>C	c.(772-774)CCT>CCC	p.P258P	UBAP1_uc010mka.1_Silent_p.P294P|UBAP1_uc003zty.2_Silent_p.P258P|UBAP1_uc011loi.1_Silent_p.P294P|UBAP1_uc011loj.1_Silent_p.P322P|KIF24_uc010mkb.2_Intron|UBAP1_uc003ztz.2_Silent_p.P258P	NM_016525	NP_057609	Q9NZ09	UBAP1_HUMAN	ubiquitin associated protein 1	258						cytoplasm					0			LUSC - Lung squamous cell carcinoma(29;0.00272)															---	---	---	---
KIAA1161	57462	broad.mit.edu	37	9	34371882	34371882	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34371882C>T	uc003zue.3	-	3	1227	c.1060G>A	c.(1060-1062)GAC>AAC	p.D354N		NM_020702	NP_065753	Q6NSJ0	K1161_HUMAN	hypothetical protein LOC57462	354	Extracellular (Potential).				carbohydrate metabolic process	integral to membrane	hydrolase activity, hydrolyzing O-glycosyl compounds			ovary(1)|breast(1)|central_nervous_system(1)	3			LUSC - Lung squamous cell carcinoma(29;0.0107)	GBM - Glioblastoma multiforme(74;0.126)														---	---	---	---
DNAI1	27019	broad.mit.edu	37	9	34490498	34490498	+	Intron	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34490498C>A	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				---	---	---	---
CNTFR	1271	broad.mit.edu	37	9	34557874	34557874	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34557874A>C	uc003zup.1	-	5	709	c.428T>G	c.(427-429)GTG>GGG	p.V143G	CNTFR_uc003zuq.1_Missense_Mutation_p.V143G	NM_147164	NP_671693	P26992	CNTFR_HUMAN	ciliary neurotrophic factor receptor	143	Fibronectin type-III 1.				nervous system development	anchored to membrane|extrinsic to membrane|plasma membrane	ciliary neurotrophic factor receptor activity|receptor binding			ovary(3)|central_nervous_system(1)|skin(1)	5	all_epithelial(49;0.0899)		STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.00494)														---	---	---	---
TLN1	7094	broad.mit.edu	37	9	35724210	35724210	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35724210C>A	uc003zxt.2	-	6	987	c.633G>T	c.(631-633)CAG>CAT	p.Q211H	TLN1_uc003zxu.3_Missense_Mutation_p.Q211H	NM_006289	NP_006280	Q9Y490	TLN1_HUMAN	talin 1	211	FERM.				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)															---	---	---	---
PGM5	5239	broad.mit.edu	37	9	71094454	71094454	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71094454G>A	uc004agr.2	+	8	1509	c.1280G>A	c.(1279-1281)CGC>CAC	p.R427H		NM_021965	NP_068800	Q15124	PGM5_HUMAN	phosphoglucomutase 5	427					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																		---	---	---	---
PRKACG	5568	broad.mit.edu	37	9	71628565	71628565	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71628565G>A	uc004agy.2	-	1	475	c.444C>T	c.(442-444)GCC>GCT	p.A148A		NM_002732	NP_002723	P22612	KAPCG_HUMAN	protein kinase, cAMP-dependent, catalytic,	148	Protein kinase.				activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|gluconeogenesis|intracellular protein kinase cascade|male gonad development|nerve growth factor receptor signaling pathway|regulation of insulin secretion|spermatogenesis|transmembrane transport|triglyceride catabolic process|water transport	cytosol|nucleoplasm	ATP binding|cAMP-dependent protein kinase activity			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
SMC5	23137	broad.mit.edu	37	9	72967215	72967215	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72967215C>T	uc004ahr.2	+	25	3391	c.3274C>T	c.(3274-3276)CGG>TGG	p.R1092W	SMC5_uc011lry.1_Missense_Mutation_p.R237W	NM_015110	NP_055925	Q8IY18	SMC5_HUMAN	SMC5 protein	1092					DNA recombination|DNA repair	chromosome|nucleus	ATP binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
TRPM6	140803	broad.mit.edu	37	9	77400926	77400926	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77400926C>T	uc004ajl.1	-	21	3021	c.2783G>A	c.(2782-2784)CGA>CAA	p.R928Q	TRPM6_uc004ajk.1_Missense_Mutation_p.R923Q|TRPM6_uc010mpb.1_RNA|TRPM6_uc010mpc.1_Intron|TRPM6_uc010mpd.1_Intron|TRPM6_uc010mpe.1_Intron|TRPM6_uc004ajm.1_Missense_Mutation_p.R214Q	NM_017662	NP_060132	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel,	928	Extracellular (Potential).				response to toxin	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|stomach(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	8																		---	---	---	---
C9orf41	138199	broad.mit.edu	37	9	77611435	77611435	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77611435C>T	uc004ajq.2	-	6	1105	c.952G>A	c.(952-954)GCT>ACT	p.A318T	uc004ajp.2_RNA|C9orf41_uc011lsi.1_RNA	NM_152420	NP_689633	Q8N4J0	CI041_HUMAN	hypothetical protein LOC138199	318										ovary(1)|skin(1)	2																		---	---	---	---
FRMD3	257019	broad.mit.edu	37	9	85926824	85926824	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85926824T>C	uc004ams.1	-	8	953	c.751A>G	c.(751-753)AAG>GAG	p.K251E	FRMD3_uc004amr.1_Missense_Mutation_p.K237E	NM_174938	NP_777598	A2A2Y4	FRMD3_HUMAN	FERM domain containing 3	251	FERM.					cytoplasm|cytoskeleton|extrinsic to membrane|integral to membrane	cytoskeletal protein binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
CDK20	23552	broad.mit.edu	37	9	90586219	90586219	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90586219C>A	uc004apr.2	-	3	527	c.221G>T	c.(220-222)GGT>GTT	p.G74V	CDK20_uc004aps.2_Missense_Mutation_p.G74V|CDK20_uc004apt.2_Missense_Mutation_p.G87V|CDK20_uc004apu.2_Missense_Mutation_p.G74V	NM_001039803	NP_001034892	Q8IZL9	CDK20_HUMAN	cell cycle related kinase isoform 3	74	Protein kinase.				cell division|multicellular organismal development	cilium|mitochondrion|nucleus	ATP binding|cyclin-dependent protein kinase activity			skin(1)	1																		---	---	---	---
ASPN	54829	broad.mit.edu	37	9	95228829	95228829	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95228829G>A	uc004ase.1	-	4	656	c.412C>T	c.(412-414)CTA>TTA	p.L138L	CENPP_uc004arz.2_Intron|CENPP_uc010mqx.2_Intron|ASPN_uc010mqy.1_Silent_p.L138L	NM_017680	NP_060150	Q9BXN1	ASPN_HUMAN	asporin precursor	138	LRR 2.				bone mineralization|negative regulation of tooth mineralization|negative regulation of transforming growth factor beta receptor signaling pathway	proteinaceous extracellular matrix	calcium ion binding				0																		---	---	---	---
ECM2	1842	broad.mit.edu	37	9	95277139	95277139	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95277139C>A	uc004ash.2	-	4	893	c.828G>T	c.(826-828)GAG>GAT	p.E276D	CENPP_uc004arz.2_Intron|CENPP_uc010mqx.2_Intron|ECM2_uc004asf.3_Missense_Mutation_p.E254D|ECM2_uc011lty.1_Missense_Mutation_p.E276D|ECM2_uc004asg.2_Missense_Mutation_p.E254D	NM_001393	NP_001384	O94769	ECM2_HUMAN	extracellular matrix protein 2 precursor	276	Poly-Glu.				cell-matrix adhesion		integrin binding			ovary(1)|skin(1)	2																		---	---	---	---
ECM2	1842	broad.mit.edu	37	9	95277140	95277140	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95277140T>C	uc004ash.2	-	4	892	c.827A>G	c.(826-828)GAG>GGG	p.E276G	CENPP_uc004arz.2_Intron|CENPP_uc010mqx.2_Intron|ECM2_uc004asf.3_Missense_Mutation_p.E254G|ECM2_uc011lty.1_Missense_Mutation_p.E276G|ECM2_uc004asg.2_Missense_Mutation_p.E254G	NM_001393	NP_001384	O94769	ECM2_HUMAN	extracellular matrix protein 2 precursor	276	Poly-Glu.				cell-matrix adhesion		integrin binding			ovary(1)|skin(1)	2																		---	---	---	---
HSD17B3	3293	broad.mit.edu	37	9	99007657	99007657	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99007657C>T	uc004awa.1	-	8	624	c.576G>A	c.(574-576)TGG>TGA	p.W192*	HSD17B3_uc010msc.1_Nonsense_Mutation_p.W192*	NM_000197	NP_000188	P37058	DHB3_HUMAN	estradiol 17 beta-dehydrogenase 3	192					androgen biosynthetic process|male genitalia development	endoplasmic reticulum membrane|microsome	binding|testosterone 17-beta-dehydrogenase (NAD+) activity|testosterone 17-beta-dehydrogenase (NADP+) activity				0		Acute lymphoblastic leukemia(62;0.0171)|all_hematologic(171;0.214)			NADH(DB00157)													---	---	---	---
GRIN3A	116443	broad.mit.edu	37	9	104335800	104335800	+	Intron	SNP	G	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104335800G>C	uc004bbp.1	-						GRIN3A_uc004bbo.1_Intron	NM_133445	NP_597702			glutamate receptor, ionotropic,						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|neuron projection|neuronal cell body|outer membrane-bounded periplasmic space|postsynaptic density|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|glycine binding|identical protein binding|N-methyl-D-aspartate selective glutamate receptor activity|protein phosphatase 2A binding			ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1)	7		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Ketamine(DB01221)|L-Glutamic Acid(DB00142)|Memantine(DB01043)|Meperidine(DB00454)|Methadone(DB00333)|Orphenadrine(DB01173)|Procaine(DB00721)|Riluzole(DB00740)													---	---	---	---
GRIN3A	116443	broad.mit.edu	37	9	104499795	104499795	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104499795G>A	uc004bbp.1	-	1	1068	c.467C>T	c.(466-468)GCA>GTA	p.A156V	GRIN3A_uc004bbq.1_Missense_Mutation_p.A156V	NM_133445	NP_597702	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic,	156	Extracellular (Potential).				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)													---	---	---	---
SMC2	10592	broad.mit.edu	37	9	106901507	106901507	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106901507G>A	uc004bbv.2	+	25	3793	c.3505G>A	c.(3505-3507)GCC>ACC	p.A1169T	SMC2_uc004bbw.2_Missense_Mutation_p.A1169T|SMC2_uc011lvl.1_Missense_Mutation_p.A1169T|SMC2_uc004bbx.2_Missense_Mutation_p.A1169T|SMC2_uc004bby.2_RNA	NM_001042551	NP_001036016	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	1169					cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism	condensin complex|cytoplasm|nuclear chromosome	ATP binding|protein heterodimerization activity			ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1)	9																		---	---	---	---
ABCA1	19	broad.mit.edu	37	9	107558369	107558369	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107558369C>T	uc004bcl.2	-	39	5660	c.5347G>A	c.(5347-5349)GTG>ATG	p.V1783M		NM_005502	NP_005493	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A member 1	1783	Helical; (Potential).				Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|lung(4)|ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	17				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)													---	---	---	---
ZNF462	58499	broad.mit.edu	37	9	109686851	109686851	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109686851C>A	uc004bcz.2	+	3	947	c.658C>A	c.(658-660)CCA>ACA	p.P220T	ZNF462_uc010mto.2_Missense_Mutation_p.P68T|ZNF462_uc004bda.2_Missense_Mutation_p.P68T	NM_021224	NP_067047	Q96JM2	ZN462_HUMAN	zinc finger protein 462	220					transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(5)	5																		---	---	---	---
PALM2-AKAP2	445815	broad.mit.edu	37	9	112686016	112686016	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112686016C>T	uc004bei.2	+	4	451	c.259C>T	c.(259-261)CTG>TTG	p.L87L	PALM2_uc004bef.2_Silent_p.L89L|PALM2_uc004beg.2_Silent_p.L89L|PALM2_uc004beh.3_Silent_p.L87L|PALM2-AKAP2_uc004bek.3_Silent_p.L87L|PALM2-AKAP2_uc004bej.3_Silent_p.L87L|PALM2-AKAP2_uc004bel.1_5'UTR	NM_001136562	NP_001130034	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2 isoform 2	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment							enzyme binding			ovary(3)|central_nervous_system(2)|skin(1)	6																		---	---	---	---
PALM2-AKAP2	445815	broad.mit.edu	37	9	112900738	112900738	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112900738C>T	uc004bei.2	+	9	3802	c.3610C>T	c.(3610-3612)CAA>TAA	p.Q1204*	PALM2-AKAP2_uc004bek.3_Nonsense_Mutation_p.Q972*|PALM2-AKAP2_uc004bej.3_Nonsense_Mutation_p.Q972*|PALM2-AKAP2_uc004bel.1_Nonsense_Mutation_p.Q782*|AKAP2_uc011lwi.1_Nonsense_Mutation_p.Q830*|AKAP2_uc004bem.2_Nonsense_Mutation_p.Q830*|PALM2-AKAP2_uc010mtw.1_Nonsense_Mutation_p.Q790*|AKAP2_uc011lwj.1_Nonsense_Mutation_p.Q741*|PALM2-AKAP2_uc004ben.2_Nonsense_Mutation_p.Q741*	NM_001136562	NP_001130034	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2 isoform 2	741	Potential.						enzyme binding			ovary(3)|central_nervous_system(2)|skin(1)	6																		---	---	---	---
C9orf152	401546	broad.mit.edu	37	9	112963424	112963424	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112963424G>A	uc011lwk.1	-	2	1078	c.524C>T	c.(523-525)GCT>GTT	p.A175V		NM_001012993	NP_001013011	Q5JTZ5	CI152_HUMAN	hypothetical protein LOC401546	175											0																		---	---	---	---
MUSK	4593	broad.mit.edu	37	9	113459685	113459685	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113459685A>G	uc004bey.2	+	5	665	c.567A>G	c.(565-567)CGA>CGG	p.R189R	MUSK_uc004bex.2_Silent_p.R189R	NM_005592	NP_005583	O15146	MUSK_HUMAN	skeletal muscle receptor tyrosine kinase	189	Ig-like 2.|Extracellular (Potential).				transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(3)|ovary(2)|central_nervous_system(1)	6																		---	---	---	---
ROD1	9991	broad.mit.edu	37	9	115024841	115024841	+	Silent	SNP	T	C	C	rs140763640	byFrequency	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115024841T>C	uc004bfw.2	-	6	661	c.474A>G	c.(472-474)CAA>CAG	p.Q158Q	ROD1_uc004bfv.2_Silent_p.Q164Q|ROD1_uc004bfx.2_Silent_p.Q161Q|ROD1_uc011lwu.1_Silent_p.Q130Q|ROD1_uc004bfy.2_Silent_p.Q63Q|ROD1_uc004bfz.2_Silent_p.Q130Q	NM_005156	NP_005147	O95758	ROD1_HUMAN	ROD1 regulator of differentiation 1 isoform 1	158					anatomical structure morphogenesis|mRNA processing	nucleus	nucleotide binding|RNA binding			skin(1)	1																		---	---	---	---
FKBP15	23307	broad.mit.edu	37	9	115933961	115933961	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115933961G>A	uc004bgs.2	-	24	2676	c.2558C>T	c.(2557-2559)ACA>ATA	p.T853I	FKBP15_uc004bgr.2_Missense_Mutation_p.T290I|FKBP15_uc011lxc.1_Missense_Mutation_p.T434I|FKBP15_uc011lxd.1_Missense_Mutation_p.T785I	NM_015258	NP_056073	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	853	Potential.				endocytosis|protein folding	axon|early endosome	actin binding			ovary(3)	3																		---	---	---	---
KIF12	113220	broad.mit.edu	37	9	116854636	116854636	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116854636G>A	uc004bif.2	-	15	1617	c.1379C>T	c.(1378-1380)CCG>CTG	p.P460L	KIF12_uc004big.2_RNA	NM_138424	NP_612433	Q96FN5	KIF12_HUMAN	kinesin family member 12	593	Pro-rich.				microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity				0																		---	---	---	---
PAPPA	5069	broad.mit.edu	37	9	118950436	118950436	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118950436C>T	uc004bjn.2	+	2	1800	c.1419C>T	c.(1417-1419)TGC>TGT	p.C473C	PAPPA_uc011lxp.1_Silent_p.C266C|PAPPA_uc011lxq.1_Silent_p.C266C	NM_002581	NP_002572	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A	473	Metalloprotease.				cell differentiation|female pregnancy	cytoplasm|extracellular region|membrane	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(4)|pancreas(1)	9																		---	---	---	---
ASTN2	23245	broad.mit.edu	37	9	119802238	119802238	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119802238A>G	uc004bjs.1	-	6	1384	c.1283T>C	c.(1282-1284)CTG>CCG	p.L428P	ASTN2_uc004bjr.1_Missense_Mutation_p.L428P|ASTN2_uc004bjt.1_Missense_Mutation_p.L377P	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c	428	Cytoplasmic (Potential).					integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9																		---	---	---	---
MEGF9	1955	broad.mit.edu	37	9	123476053	123476053	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123476053G>T	uc004bkj.1	-	1	560	c.560C>A	c.(559-561)CCC>CAC	p.P187H	MEGF9_uc011lyb.1_Missense_Mutation_p.P187H|MEGF9_uc004bkk.3_Missense_Mutation_p.P187H	NM_001080497	NP_001073966	Q9H1U4	MEGF9_HUMAN	multiple EGF-like-domains 9	195	Extracellular (Potential).|Pro-rich.					integral to membrane	calcium ion binding				0																		---	---	---	---
CEP110	11064	broad.mit.edu	37	9	123900864	123900864	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123900864G>A	uc004bkx.1	+	14	2275	c.2244G>A	c.(2242-2244)AGG>AGA	p.R748R	CEP110_uc004bky.1_Silent_p.R352R|CEP110_uc004bkz.1_Silent_p.R196R|CEP110_uc004bla.1_Silent_p.R196R	NM_007018	NP_008949	Q7Z7A1	CNTRL_HUMAN	centrosomal protein 110kDa	748	Potential.				cell division|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein binding				0																		---	---	---	---
NDUFA8	4702	broad.mit.edu	37	9	124906668	124906668	+	Intron	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124906668T>C	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)													---	---	---	---
OLFML2A	169611	broad.mit.edu	37	9	127570250	127570250	+	Intron	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127570250G>T	uc004bov.2	+						OLFML2A_uc004bow.2_Intron	NM_182487	NP_872293			olfactomedin-like 2A precursor												0																		---	---	---	---
FAM125B	89853	broad.mit.edu	37	9	129157932	129157932	+	Silent	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129157932T>G	uc004bqh.1	+	6	699	c.618T>G	c.(616-618)CCT>CCG	p.P206P	FAM125B_uc004bqg.1_Silent_p.P206P|FAM125B_uc011lzy.1_Silent_p.P191P|FAM125B_uc010mxd.2_Silent_p.P199P|FAM125B_uc011lzz.1_Silent_p.P199P	NM_033446	NP_258257	Q9H7P6	F125B_HUMAN	hypothetical protein LOC89853 isoform 1	206					protein transport	late endosome membrane					0																		---	---	---	---
ZBTB43	23099	broad.mit.edu	37	9	129595631	129595631	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129595631G>A	uc004bql.2	+	3	1116	c.843G>A	c.(841-843)ACG>ACA	p.T281T	ZBTB43_uc010mxf.2_Silent_p.T281T	NM_014007	NP_054726	O43298	ZBT43_HUMAN	zinc finger and BTB domain containing 43	281					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
SH2D3C	10044	broad.mit.edu	37	9	130511736	130511736	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130511736C>T	uc004bsc.2	-	5	1035	c.893G>A	c.(892-894)CGC>CAC	p.R298H	SH2D3C_uc010mxo.2_Missense_Mutation_p.R138H|SH2D3C_uc004bry.2_Missense_Mutation_p.R140H|SH2D3C_uc004brz.3_5'UTR|SH2D3C_uc011mak.1_5'UTR|SH2D3C_uc004bsa.2_Missense_Mutation_p.R141H|SH2D3C_uc004bsb.2_Missense_Mutation_p.R230H	NM_170600	NP_733745	Q8N5H7	SH2D3_HUMAN	SH2 domain containing 3C isoform a	298	SH2.				JNK cascade|small GTPase mediated signal transduction	cytoplasm|membrane	guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			ovary(1)	1																		---	---	---	---
SLC25A25	114789	broad.mit.edu	37	9	130869685	130869685	+	Missense_Mutation	SNP	G	A	A	rs146124484		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130869685G>A	uc004bte.2	+	10	1401	c.1372G>A	c.(1372-1374)GAG>AAG	p.E458K	SLC25A25_uc004btb.2_Missense_Mutation_p.E492K|SLC25A25_uc004btc.2_Missense_Mutation_p.E478K|SLC25A25_uc004btd.2_Missense_Mutation_p.E490K|SLC25A25_uc004btf.2_Missense_Mutation_p.E355K	NM_052901	NP_443133	Q6KCM7	SCMC2_HUMAN	solute carrier family 25, member 25 isoform a	458	Solcar 3.|Mitochondrial intermembrane (Potential).				transmembrane transport	integral to membrane|mitochondrial inner membrane	calcium ion binding				0																		---	---	---	---
LRRC8A	56262	broad.mit.edu	37	9	131670167	131670167	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131670167G>A	uc004bwl.3	+	3	978	c.724G>A	c.(724-726)GCG>ACG	p.A242T	LRRC8A_uc010myp.2_Missense_Mutation_p.A242T|LRRC8A_uc010myq.2_Missense_Mutation_p.A242T	NM_019594	NP_062540	Q8IWT6	LRC8A_HUMAN	leucine rich repeat containing 8 family, member	242					pre-B cell differentiation	integral to membrane					0																		---	---	---	---
FAM73B	84895	broad.mit.edu	37	9	131825860	131825860	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131825860G>T	uc004bxa.2	+	11	1306	c.1120G>T	c.(1120-1122)GGG>TGG	p.G374W	FAM73B_uc004bwy.2_RNA|FAM73B_uc004bwz.2_Intron|FAM73B_uc011mbn.1_Missense_Mutation_p.G374W	NM_032809	NP_116198	Q7L4E1	FA73B_HUMAN	hypothetical protein LOC84895	374						integral to membrane				skin(1)	1																		---	---	---	---
DOLPP1	57171	broad.mit.edu	37	9	131847556	131847556	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131847556C>T	uc004bxc.2	+	4	361	c.333C>T	c.(331-333)TCC>TCT	p.S111S	DOLPP1_uc004bxd.2_Silent_p.S111S|DOLPP1_uc004bxe.2_RNA|DOLPP1_uc004bxf.2_5'Flank	NM_020438	NP_065171	Q86YN1	DOPP1_HUMAN	dolichyl pyrophosphate phosphatase 1 isoform a	111	Helical; (Potential).				dolichyl diphosphate biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to endoplasmic reticulum membrane	dolichyldiphosphatase activity			skin(1)	1																		---	---	---	---
POMT1	10585	broad.mit.edu	37	9	134381507	134381507	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134381507C>T	uc004cav.2	+	3	331	c.129C>T	c.(127-129)GAC>GAT	p.D43D	POMT1_uc011mci.1_Silent_p.D43D|POMT1_uc004cax.2_Silent_p.D43D|POMT1_uc011mcj.1_Intron|POMT1_uc004cau.2_Silent_p.D43D|POMT1_uc004caw.2_Translation_Start_Site|POMT1_uc011mck.1_Intron|POMT1_uc011mcl.1_Intron|POMT1_uc011mcm.1_Intron	NM_007171	NP_009102	Q9Y6A1	POMT1_HUMAN	protein-O-mannosyltransferase 1 isoform a	43	Helical; (Potential).				multicellular organismal development|protein O-linked glycosylation	endoplasmic reticulum membrane|integral to membrane	dolichyl-phosphate-mannose-protein mannosyltransferase activity|metal ion binding			upper_aerodigestive_tract(1)	1		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.65e-05)|Epithelial(140;0.000259)														---	---	---	---
UCK1	83549	broad.mit.edu	37	9	134400618	134400618	+	Intron	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134400618G>A	uc004cay.2	-						UCK1_uc010mzk.2_Intron|UCK1_uc004cba.2_Intron|UCK1_uc004caz.2_Intron	NM_031432	NP_113620			uridine-cytidine kinase 1 isoform a						pyrimidine base metabolic process|pyrimidine nucleoside salvage	cytosol	ATP binding|phosphotransferase activity, alcohol group as acceptor|uridine kinase activity				0				OV - Ovarian serous cystadenocarcinoma(145;2.34e-05)|Epithelial(140;0.000219)														---	---	---	---
SETX	23064	broad.mit.edu	37	9	135204576	135204576	+	Silent	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135204576A>C	uc004cbk.2	-	10	2592	c.2409T>G	c.(2407-2409)ACT>ACG	p.T803T	SETX_uc004cbj.2_Silent_p.T422T|SETX_uc010mzt.2_Silent_p.T422T	NM_015046	NP_055861	Q7Z333	SETX_HUMAN	senataxin	803					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)														---	---	---	---
SURF4	6836	broad.mit.edu	37	9	136233468	136233468	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136233468C>T	uc004cdj.2	-						SURF4_uc011mda.1_Intron|SURF4_uc010nal.2_Intron|SURF4_uc011mdb.1_Intron|SURF4_uc011mdc.1_Intron|SURF4_uc011mdd.1_Intron	NM_033161	NP_149351			surfeit 4							endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane	protein binding				0				OV - Ovarian serous cystadenocarcinoma(145;5.32e-07)|Epithelial(140;4.56e-06)|all cancers(34;4.25e-05)														---	---	---	---
NOTCH1	4851	broad.mit.edu	37	9	139391228	139391228	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139391228G>A	uc004chz.2	-	34	6963	c.6963C>T	c.(6961-6963)AAC>AAT	p.N2321N		NM_017617	NP_060087	P46531	NOTC1_HUMAN	notch1 preproprotein	2321	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)			---	---	---	---
ZMYND19	116225	broad.mit.edu	37	9	140481507	140481507	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140481507C>T	uc004cno.1	-	4	493	c.271G>A	c.(271-273)GCT>ACT	p.A91T		NM_138462	NP_612471	Q96E35	ZMY19_HUMAN	zinc finger, MYND domain containing 19	91						Golgi apparatus|plasma membrane	zinc ion binding			skin(1)	1	all_cancers(76;0.106)			OV - Ovarian serous cystadenocarcinoma(145;0.000275)|Epithelial(140;0.00047)														---	---	---	---
CACNA1B	774	broad.mit.edu	37	9	140901278	140901278	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140901278C>T	uc004cog.2	+	16	2179	c.2034C>T	c.(2032-2034)GGC>GGT	p.G678G	CACNA1B_uc011mfd.1_Silent_p.G209G	NM_000718	NP_000709	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type,	678	Extracellular (Potential).|II.				membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	ATP binding|protein C-terminus binding|voltage-gated calcium channel activity			breast(3)|large_intestine(2)|ovary(1)	6	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)													---	---	---	---
DIP2C	22982	broad.mit.edu	37	10	395337	395337	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:395337C>T	uc001ifp.2	-	25	3133	c.3043G>A	c.(3043-3045)GCC>ACC	p.A1015T	DIP2C_uc009xhi.1_Missense_Mutation_p.A401T	NM_014974	NP_055789	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C	1015						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)														---	---	---	---
C10orf18	54906	broad.mit.edu	37	10	5782269	5782269	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5782269C>T	uc001iij.2	+	13	2761	c.2136C>T	c.(2134-2136)GAC>GAT	p.D712D	C10orf18_uc001iik.2_Intron	NM_017782	NP_060252	Q5VWN6	CJ018_HUMAN	hypothetical protein LOC54906	712										ovary(1)|central_nervous_system(1)	2																		---	---	---	---
C10orf18	54906	broad.mit.edu	37	10	5784337	5784337	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5784337C>T	uc001iij.2	+	14	3230	c.2605C>T	c.(2605-2607)CGT>TGT	p.R869C	C10orf18_uc001iik.2_Intron	NM_017782	NP_060252	Q5VWN6	CJ018_HUMAN	hypothetical protein LOC54906	869										ovary(1)|central_nervous_system(1)	2																		---	---	---	---
ACBD7	414149	broad.mit.edu	37	10	15120521	15120521	+	3'UTR	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15120521G>T	uc001inv.2	-	4					ACBD7_uc010qby.1_Intron	NM_001039844	NP_001034933			acyl-Coenzyme A binding domain containing 7								fatty-acyl-CoA binding				0																		---	---	---	---
MYO3A	53904	broad.mit.edu	37	10	26286158	26286158	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26286158C>T	uc001isn.2	+	6	839	c.479C>T	c.(478-480)ACG>ATG	p.T160M	MYO3A_uc009xko.1_Missense_Mutation_p.T160M|MYO3A_uc009xkp.1_RNA|MYO3A_uc009xkq.1_Missense_Mutation_p.T160M|MYO3A_uc001ism.2_Missense_Mutation_p.T160M	NM_017433	NP_059129	Q8NEV4	MYO3A_HUMAN	myosin IIIA	160	Protein kinase.				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																		---	---	---	---
ARMC4	55130	broad.mit.edu	37	10	28229512	28229512	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28229512A>C	uc009xky.2	-	13	2064	c.1966T>G	c.(1966-1968)TTG>GTG	p.L656V	ARMC4_uc010qds.1_Missense_Mutation_p.L181V|ARMC4_uc010qdt.1_Missense_Mutation_p.L348V|ARMC4_uc001itz.2_Missense_Mutation_p.L656V|ARMC4_uc010qdu.1_Missense_Mutation_p.L348V	NM_018076	NP_060546	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	656	ARM 3.						binding			ovary(4)|skin(2)	6																		---	---	---	---
KIAA1462	57608	broad.mit.edu	37	10	30318203	30318203	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30318203G>A	uc001iux.2	-	2	933	c.874C>T	c.(874-876)CCC>TCC	p.P292S	KIAA1462_uc001iuy.2_Intron|KIAA1462_uc001iuz.2_Missense_Mutation_p.P154S|KIAA1462_uc009xle.1_Missense_Mutation_p.P292S	NM_020848	NP_065899	Q9P266	K1462_HUMAN	hypothetical protein LOC57608	292	Pro-rich.									ovary(4)	4																		---	---	---	---
ANKRD30A	91074	broad.mit.edu	37	10	37422892	37422892	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37422892C>T	uc001iza.1	+	5	597	c.498C>T	c.(496-498)GGC>GGT	p.G166G		NM_052997	NP_443723	Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	222	ANK 5.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(7)|breast(1)|skin(1)	9																		---	---	---	---
CSGALNACT2	55454	broad.mit.edu	37	10	43678815	43678815	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43678815G>T	uc001jan.2	+	8	1789	c.1454G>T	c.(1453-1455)TGG>TTG	p.W485L		NM_018590	NP_061060	Q8N6G5	CGAT2_HUMAN	chondroitin sulfate	485	Lumenal (Potential).				chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|dermatan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process	Golgi cisterna membrane|integral to Golgi membrane	glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding			ovary(1)	1																		---	---	---	---
C10orf10	11067	broad.mit.edu	37	10	45473007	45473007	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45473007G>A	uc001jbr.3	-	2	762	c.472C>T	c.(472-474)CCT>TCT	p.P158S	RASSF4_uc001jbo.2_Intron|RASSF4_uc001jbp.2_Intron|RASSF4_uc009xmn.2_Intron|RASSF4_uc001jbq.2_Intron	NM_007021	NP_008952	Q9NTK1	DEPP_HUMAN	fasting-induced protein	158						mitochondrion					0																		---	---	---	---
RASSF4	83937	broad.mit.edu	37	10	45480361	45480361	+	Missense_Mutation	SNP	G	T	T	rs35672435	byFrequency	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45480361G>T	uc001jbo.2	+	6	608	c.474G>T	c.(472-474)GAG>GAT	p.E158D	RASSF4_uc001jbp.2_Missense_Mutation_p.E189D|RASSF4_uc009xmn.2_Missense_Mutation_p.E88D|RASSF4_uc001jbq.2_Missense_Mutation_p.E55D|RASSF4_uc001jbt.2_Missense_Mutation_p.E115D	NM_032023	NP_114412	Q9H2L5	RASF4_HUMAN	Ras association domain family 4	158					cell cycle|signal transduction		protein binding			large_intestine(1)	1																		---	---	---	---
OR13A1	79290	broad.mit.edu	37	10	45798956	45798956	+	Silent	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45798956G>T	uc001jcc.1	-	4	1224	c.915C>A	c.(913-915)CCC>CCA	p.P305P	OR13A1_uc001jcd.1_Silent_p.P301P	NM_001004297	NP_001004297	Q8NGR1	O13A1_HUMAN	olfactory receptor, family 13, subfamily A,	305	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0																		---	---	---	---
PARG	8505	broad.mit.edu	37	10	51581263	51581263	+	Intron	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51581263T>C	uc001jih.2	-						uc010qha.1_Intron|uc001jin.2_Intron|uc010qhb.1_Intron|uc010qhc.1_Intron|NCOA4_uc009xon.2_Intron|NCOA4_uc010qhd.1_Intron|NCOA4_uc001jis.3_Intron|NCOA4_uc010qhe.1_Intron|NCOA4_uc010qhf.1_Intron|NCOA4_uc001jit.2_Intron|NCOA4_uc009xoo.2_Intron	NM_003631	NP_003622			poly (ADP-ribose) glycohydrolase						carbohydrate metabolic process	nucleus	poly(ADP-ribose) glycohydrolase activity			ovary(2)	2				Epithelial(53;0.213)														---	---	---	---
RTKN2	219790	broad.mit.edu	37	10	63995887	63995887	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63995887T>C	uc001jlw.2	-	6	721	c.624A>G	c.(622-624)AAA>AAG	p.K208K	RTKN2_uc009xpf.1_5'UTR	NM_145307	NP_660350	Q8IZC4	RTKN2_HUMAN	rhotekin 2	208					signal transduction	intracellular					0	Prostate(12;0.0297)|all_hematologic(501;0.215)																	---	---	---	---
TET1	80312	broad.mit.edu	37	10	70404511	70404511	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70404511T>C	uc001jok.3	+	4	2530	c.2025T>C	c.(2023-2025)AGT>AGC	p.S675S		NM_030625	NP_085128	Q8NFU7	TET1_HUMAN	CXXC finger 6	675					DNA demethylation|inner cell mass cell differentiation|negative regulation of methylation-dependent chromatin silencing|stem cell maintenance		iron ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|structure-specific DNA binding|zinc ion binding			ovary(5)|lung(2)|prostate(1)|breast(1)	9																		---	---	---	---
STOX1	219736	broad.mit.edu	37	10	70644170	70644170	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70644170G>A	uc001jos.2	+	3	705	c.618G>A	c.(616-618)CTG>CTA	p.L206L	STOX1_uc001jor.2_Silent_p.L206L|STOX1_uc009xpy.2_Intron|STOX1_uc001joq.2_Silent_p.L96L	NM_001130161	NP_001123633	Q6ZVD7	STOX1_HUMAN	storkhead box 1 isoform a	206						cytoplasm|nucleolus	DNA binding			kidney(1)|skin(1)	2																		---	---	---	---
ADAMTS14	140766	broad.mit.edu	37	10	72517998	72517998	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72517998G>A	uc001jrh.2	+	21	3135	c.3135G>A	c.(3133-3135)GTG>GTA	p.V1045V	ADAMTS14_uc001jrg.2_Silent_p.V1048V	NM_080722	NP_542453	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1045					collagen catabolic process|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|upper_aerodigestive_tract(1)	6																		---	---	---	---
SLC29A3	55315	broad.mit.edu	37	10	73104043	73104043	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73104043C>T	uc001jrr.3	+	3	435	c.378C>T	c.(376-378)GTC>GTT	p.V126V	SLC29A3_uc001jrs.3_Silent_p.V126V|SLC29A3_uc010qjq.1_Intron|SLC29A3_uc001jrt.3_Intron|SLC29A3_uc001jru.3_Intron	NM_018344	NP_060814	Q9BZD2	S29A3_HUMAN	solute carrier family 29 (nucleoside	126	Helical; (Potential).				nucleobase, nucleoside and nucleotide metabolic process	integral to membrane|late endosome membrane|lysosomal membrane	nucleoside transmembrane transporter activity				0																		---	---	---	---
TTC18	118491	broad.mit.edu	37	10	75053088	75053088	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75053088A>G	uc009xrc.2	-	17	2034	c.1913T>C	c.(1912-1914)CTT>CCT	p.L638P	TTC18_uc001jty.2_Missense_Mutation_p.L638P|TTC18_uc009xrd.1_3'UTR|TTC18_uc001jtv.3_5'Flank|TTC18_uc001jtw.3_5'Flank|TTC18_uc001jtx.2_Missense_Mutation_p.L19P	NM_145170	NP_660153	Q5T0N1	TTC18_HUMAN	tetratricopeptide repeat domain 18	638	TPR 1.						binding			ovary(2)|central_nervous_system(1)	3	Prostate(51;0.0119)																	---	---	---	---
USP54	159195	broad.mit.edu	37	10	75289942	75289942	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75289942T>C	uc001juo.2	-	12	1804	c.1787A>G	c.(1786-1788)CAC>CGC	p.H596R	USP54_uc001juk.2_5'UTR|USP54_uc001jul.2_5'UTR|USP54_uc001jum.2_RNA|USP54_uc001jun.2_RNA|USP54_uc001jup.2_Missense_Mutation_p.H596R|USP54_uc010qkl.1_Missense_Mutation_p.H596R	NM_152586	NP_689799	Q70EL1	UBP54_HUMAN	ubiquitin specific peptidase 54	596					ubiquitin-dependent protein catabolic process		protein binding|ubiquitin thiolesterase activity			breast(3)|lung(2)|kidney(1)	6	Prostate(51;0.0112)																	---	---	---	---
KIAA0913	23053	broad.mit.edu	37	10	75557012	75557012	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75557012C>A	uc009xrl.2	+	17	3433	c.3401C>A	c.(3400-3402)CCT>CAT	p.P1134H	KIAA0913_uc001jve.2_Missense_Mutation_p.P1139H|KIAA0913_uc001jvf.2_Missense_Mutation_p.P1134H|KIAA0913_uc001jvh.2_RNA|KIAA0913_uc001jvi.2_Missense_Mutation_p.P569H|KIAA0913_uc010qkr.1_Missense_Mutation_p.P557H|KIAA0913_uc001jvj.2_Missense_Mutation_p.P557H|KIAA0913_uc009xrn.1_5'Flank	NM_015037	NP_055852	A7E2V4	K0913_HUMAN	hypothetical protein LOC23053	1134							zinc ion binding			breast(1)	1	Prostate(51;0.0112)																	---	---	---	---
MYST4	23522	broad.mit.edu	37	10	76788886	76788886	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76788886A>G	uc001jwn.1	+	18	4797	c.4304A>G	c.(4303-4305)GAG>GGG	p.E1435G	MYST4_uc001jwo.1_Missense_Mutation_p.E1143G|MYST4_uc001jwp.1_Missense_Mutation_p.E1252G	NM_012330	NP_036462	Q8WYB5	MYST4_HUMAN	MYST histone acetyltransferase (monocytic	1435					histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1)	16	all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964)							T	CREBBP	AML								---	---	---	---
SAMD8	142891	broad.mit.edu	37	10	76910845	76910845	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76910845C>T	uc001jwx.1	+	2	662	c.559C>T	c.(559-561)CCA>TCA	p.P187S	SAMD8_uc001jwy.1_Missense_Mutation_p.P187S	NM_144660	NP_653261	Q96LT4	SAMD8_HUMAN	sterile alpha motif domain containing 8	187					sphingomyelin biosynthetic process	integral to membrane					0	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)																	---	---	---	---
GHITM	27069	broad.mit.edu	37	10	85910545	85910545	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85910545A>G	uc001kcs.1	+	8	1066	c.862A>G	c.(862-864)AGC>GGC	p.S288G	GHITM_uc010qma.1_Missense_Mutation_p.S219G|GHITM_uc010qmb.1_Missense_Mutation_p.S218G	NM_014394	NP_055209	Q9H3K2	GHITM_HUMAN	growth hormone inducible transmembrane protein	288	Helical; (Potential).				apoptosis	integral to membrane|mitochondrial inner membrane					0																		---	---	---	---
CDHR1	92211	broad.mit.edu	37	10	85968036	85968036	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85968036G>A	uc001kcv.2	+	11	1070	c.1070G>A	c.(1069-1071)AGC>AAC	p.S357N	CDHR1_uc001kcw.2_Missense_Mutation_p.S357N|CDHR1_uc009xst.2_Missense_Mutation_p.S116N	NM_033100	NP_149091	Q96JP9	CDHR1_HUMAN	protocadherin 21 precursor	357	Extracellular (Potential).				homophilic cell adhesion		calcium ion binding|receptor activity			ovary(1)	1																		---	---	---	---
AGAP11	119385	broad.mit.edu	37	10	88768819	88768819	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88768819A>G	uc001kee.2	+	12	2014	c.810A>G	c.(808-810)GAA>GAG	p.E270E	AGAP11_uc001kef.2_Intron	NM_133447	NP_597704	Q8TF27	AGA11_HUMAN	ankyrin repeat and GTPase domain Arf GTPase	270	PH.				regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding				0																		---	---	---	---
KIF20B	9585	broad.mit.edu	37	10	91469778	91469778	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91469778T>C	uc001kgs.1	+	5	518	c.446T>C	c.(445-447)TTT>TCT	p.F149S	KIF20B_uc001kgr.1_Missense_Mutation_p.F149S	NM_016195	NP_057279	Q96Q89	KI20B_HUMAN	M-phase phosphoprotein 1	149	Kinesin-motor.				cell cycle arrest|cell division|microtubule-based movement|mitosis|regulation of mitosis	centrosome|microtubule|nucleolus|nucleoplasm|spindle	ATP binding|ATPase activity|microtubule motor activity|WW domain binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
HECTD2	143279	broad.mit.edu	37	10	93251032	93251032	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93251032C>T	uc001khl.2	+	12	1367	c.1267C>T	c.(1267-1269)CGG>TGG	p.R423W	LOC100188947_uc010qnl.1_Intron|HECTD2_uc010qnm.1_Missense_Mutation_p.R427W|HECTD2_uc001khm.2_RNA|HECTD2_uc009xty.1_Missense_Mutation_p.R12W|HECTD2_uc001khn.1_Missense_Mutation_p.R73W	NM_182765	NP_877497	Q5U5R9	HECD2_HUMAN	HECT domain containing 2 isoform a	423					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	ubiquitin-protein ligase activity			skin(1)	1																		---	---	---	---
CYP2C18	1562	broad.mit.edu	37	10	96447945	96447945	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96447945G>A	uc001kjv.3	+	3	721	c.395G>A	c.(394-396)CGG>CAG	p.R132Q	CYP2C18_uc001kjw.3_Missense_Mutation_p.R132Q|CYP2C19_uc009xus.1_5'UTR|CYP2C19_uc010qny.1_5'UTR	NM_000772	NP_000763	P33260	CP2CI_HUMAN	cytochrome P450 family 2 subfamily C polypeptide	132					xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(3)|lung(1)|skin(1)	5		Colorectal(252;0.09)		all cancers(201;2.8e-06)|KIRC - Kidney renal clear cell carcinoma(50;0.0646)|Kidney(138;0.0805)														---	---	---	---
CYP2C18	1562	broad.mit.edu	37	10	96454748	96454748	+	Nonsense_Mutation	SNP	C	T	T	rs141271146		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96454748C>T	uc001kjv.3	+	4	882	c.556C>T	c.(556-558)CGA>TGA	p.R186*	CYP2C18_uc001kjw.3_Nonsense_Mutation_p.R186*|CYP2C19_uc009xus.1_Intron|CYP2C19_uc010qny.1_5'UTR	NM_000772	NP_000763	P33260	CP2CI_HUMAN	cytochrome P450 family 2 subfamily C polypeptide	186					xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(3)|lung(1)|skin(1)	5		Colorectal(252;0.09)		all cancers(201;2.8e-06)|KIRC - Kidney renal clear cell carcinoma(50;0.0646)|Kidney(138;0.0805)														---	---	---	---
CYP2C9	1559	broad.mit.edu	37	10	96745861	96745861	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96745861T>G	uc001kka.3	+	8	1246	c.1221T>G	c.(1219-1221)TTT>TTG	p.F407L	CYP2C9_uc009xut.2_Missense_Mutation_p.F405L	NM_000771	NP_000762	P11712	CP2C9_HUMAN	cytochrome P450, family 2, subfamily C,	407					exogenous drug catabolic process|monocarboxylic acid metabolic process|monoterpenoid metabolic process|oxidative demethylation|steroid metabolic process|urea metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	(S)-limonene 6-monooxygenase activity|(S)-limonene 7-monooxygenase activity|4-hydroxyacetophenone monooxygenase activity|caffeine oxidase activity|drug binding|electron carrier activity|heme binding|oxygen binding|steroid hydroxylase activity			skin(4)|ovary(2)	6		Colorectal(252;0.0902)		all cancers(201;6.93e-05)	Acenocoumarol(DB01418)|Alosetron(DB00969)|Amiodarone(DB01118)|Antihemophilic Factor(DB00025)|Aprepitant(DB00673)|Bosentan(DB00559)|Carprofen(DB00821)|Carvedilol(DB01136)|Celecoxib(DB00482)|Clomipramine(DB01242)|Dapsone(DB00250)|Delavirdine(DB00705)|Desloratadine(DB00967)|Desogestrel(DB00304)|Diclofenac(DB00586)|Esomeprazole(DB00736)|Etodolac(DB00749)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Gemfibrozil(DB01241)|Ginkgo biloba(DB01381)|Glibenclamide(DB01016)|Glimepiride(DB00222)|Glipizide(DB01067)|Guanfacine(DB01018)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Imipramine(DB00458)|Irbesartan(DB01029)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Losartan(DB00678)|Lumiracoxib(DB01283)|Marinol(DB00470)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mephenytoin(DB00532)|Metronidazole(DB00916)|Miconazole(DB01110)|Midazolam(DB00683)|Montelukast(DB00471)|Nateglinide(DB00731)|Nelfinavir(DB00220)|Nicardipine(DB00622)|Oxymorphone(DB01192)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Phenprocoumon(DB00946)|Phenytoin(DB00252)|Pravastatin(DB00175)|Quinidine(DB00908)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Sertraline(DB01104)|Sildenafil(DB00203)|Sulfamethoxazole(DB01015)|Suprofen(DB00870)|Tamoxifen(DB00675)|Tenoxicam(DB00469)|Terfenadine(DB00342)|Tolbutamide(DB01124)|Torasemide(DB00214)|Troleandomycin(DB01361)|Valdecoxib(DB00580)|Valsartan(DB00177)|Voriconazole(DB00582)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zileuton(DB00744)													---	---	---	---
SORBS1	10580	broad.mit.edu	37	10	97101418	97101418	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97101418T>C	uc001kkp.2	-	25	2492	c.2447A>G	c.(2446-2448)AAG>AGG	p.K816R	SORBS1_uc001kkk.2_Missense_Mutation_p.K310R|SORBS1_uc001kkl.2_Missense_Mutation_p.K418R|SORBS1_uc001kkn.2_Missense_Mutation_p.K581R|SORBS1_uc001kkm.2_Missense_Mutation_p.K616R|SORBS1_uc001kko.2_Missense_Mutation_p.K838R|SORBS1_uc001kkq.2_Missense_Mutation_p.K667R|SORBS1_uc001kkr.2_Missense_Mutation_p.K522R|SORBS1_uc001kks.2_Missense_Mutation_p.K466R|SORBS1_uc001kkt.2_RNA|SORBS1_uc001kku.2_Missense_Mutation_p.K563R|SORBS1_uc001kkv.2_Missense_Mutation_p.K598R|SORBS1_uc001kkw.2_Missense_Mutation_p.K770R|SORBS1_uc010qoe.1_Missense_Mutation_p.K531R|SORBS1_uc010qof.1_3'UTR	NM_001034954	NP_001030126	Q9BX66	SRBS1_HUMAN	sorbin and SH3 domain containing 1 isoform 3	816	SH3 1.				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)														---	---	---	---
BLNK	29760	broad.mit.edu	37	10	97951722	97951722	+	3'UTR	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97951722T>C	uc001kls.3	-	17					BLNK_uc001kme.3_3'UTR|BLNK_uc001klt.3_3'UTR|BLNK_uc009xvc.2_RNA|BLNK_uc001klu.3_3'UTR|BLNK_uc001klv.3_3'UTR|BLNK_uc001klw.3_RNA|BLNK_uc001klx.3_3'UTR|BLNK_uc001kly.3_3'UTR|BLNK_uc001klz.3_RNA|BLNK_uc001kma.3_3'UTR|BLNK_uc001kmb.3_3'UTR|BLNK_uc001kmc.3_RNA|BLNK_uc001kmd.3_3'UTR|BLNK_uc009xvd.2_RNA	NM_013314	NP_037446			B-cell linker isoform 1						B cell differentiation|humoral immune response|inflammatory response|intracellular signal transduction	cytoplasm|plasma membrane	SH3/SH2 adaptor activity|transmembrane receptor protein tyrosine kinase adaptor activity			skin(2)	2		Colorectal(252;0.083)		Epithelial(162;7.89e-08)|all cancers(201;2.27e-06)														---	---	---	---
LOXL4	84171	broad.mit.edu	37	10	100017808	100017808	+	Silent	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100017808G>T	uc001kpa.1	-	7	1186	c.1035C>A	c.(1033-1035)GCC>GCA	p.A345A		NM_032211	NP_115587	Q96JB6	LOXL4_HUMAN	lysyl oxidase-like 4 precursor	345	SRCR 3.					extracellular space|membrane	copper ion binding|protein binding|scavenger receptor activity			ovary(3)|breast(1)|skin(1)	5		Colorectal(252;0.234)		Epithelial(162;2.14e-11)|all cancers(201;2.49e-09)														---	---	---	---
C10orf76	79591	broad.mit.edu	37	10	103750306	103750306	+	Splice_Site	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103750306A>G	uc009xwy.1	-	19	1508	c.1406_splice	c.e19+1	p.I469_splice	C10orf76_uc009xwx.1_Splice_Site	NM_024541	NP_078817			hypothetical protein LOC79591							integral to membrane					0		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)														---	---	---	---
PPRC1	23082	broad.mit.edu	37	10	103897626	103897626	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103897626C>T	uc001kum.2	+	2	212	c.173C>T	c.(172-174)GCG>GTG	p.A58V	PPRC1_uc001kun.2_5'UTR|PPRC1_uc010qqj.1_Missense_Mutation_p.A58V|PPRC1_uc009xxa.2_5'Flank	NM_015062	NP_055877	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor	58					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleotide binding|RNA binding	p.A58A(1)		ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.122)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)														---	---	---	---
PPRC1	23082	broad.mit.edu	37	10	103898382	103898382	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103898382T>C	uc001kum.2	+	3	388	c.349T>C	c.(349-351)TTA>CTA	p.L117L	PPRC1_uc001kun.2_Intron|PPRC1_uc010qqj.1_Silent_p.L117L|PPRC1_uc009xxa.2_5'Flank	NM_015062	NP_055877	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor	117					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)														---	---	---	---
PPRC1	23082	broad.mit.edu	37	10	103906752	103906752	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103906752T>C	uc001kum.2	+	9	4042	c.4003T>C	c.(4003-4005)TTG>CTG	p.L1335L	PPRC1_uc001kun.2_Silent_p.L1215L|PPRC1_uc010qqj.1_Intron|PPRC1_uc009xxa.2_Intron	NM_015062	NP_055877	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor	1335					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)														---	---	---	---
SFXN2	118980	broad.mit.edu	37	10	104497522	104497522	+	3'UTR	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104497522G>A	uc001kwb.2	+	12					SFXN2_uc001kwc.2_RNA|SFXN2_uc001kwd.2_RNA	NM_178858	NP_849189			sideroflexin 2						iron ion homeostasis	integral to membrane	cation transmembrane transporter activity				0		Colorectal(252;0.207)		Epithelial(162;4.53e-09)|all cancers(201;1.2e-07)|BRCA - Breast invasive adenocarcinoma(275;0.218)														---	---	---	---
CNNM2	54805	broad.mit.edu	37	10	104678663	104678663	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104678663G>A	uc001kwm.2	+	1	550	c.426G>A	c.(424-426)GAG>GAA	p.E142E	CNNM2_uc001kwn.2_Silent_p.E142E|CNNM2_uc001kwl.2_Silent_p.E142E	NM_017649	NP_060119	Q9H8M5	CNNM2_HUMAN	cyclin M2 isoform 1	142					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)														---	---	---	---
TAF5	6877	broad.mit.edu	37	10	105139379	105139379	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105139379A>G	uc001kwv.2	+	4	1151	c.1128A>G	c.(1126-1128)TTA>TTG	p.L376L	TAF5_uc010qqq.1_Silent_p.L376L	NM_006951	NP_008882	Q15542	TAF5_HUMAN	TBP-associated factor 5	376					histone acetylation|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	actin cytoskeleton|transcription factor TFIID complex|transcription factor TFTC complex	protein dimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(2)	2		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;1.83e-09)|all cancers(201;1.4e-08)|BRCA - Breast invasive adenocarcinoma(275;0.198)														---	---	---	---
PDCD11	22984	broad.mit.edu	37	10	105202059	105202059	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105202059G>A	uc001kwy.1	+	32	4884	c.4797G>A	c.(4795-4797)GGG>GGA	p.G1599G		NM_014976	NP_055791	Q14690	RRP5_HUMAN	programmed cell death 11	1599	HAT 1.				mRNA processing|rRNA processing	nucleolus	RNA binding|transcription factor binding			ovary(2)|breast(2)|skin(2)|central_nervous_system(1)	7		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)														---	---	---	---
SH3PXD2A	9644	broad.mit.edu	37	10	105361982	105361982	+	Missense_Mutation	SNP	C	T	T	rs146203698		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105361982C>T	uc001kxj.1	-	14	3049	c.2909G>A	c.(2908-2910)CGG>CAG	p.R970Q	SH3PXD2A_uc010qqr.1_Intron|SH3PXD2A_uc010qqs.1_Missense_Mutation_p.R805Q|SH3PXD2A_uc010qqt.1_Missense_Mutation_p.R847Q|SH3PXD2A_uc009xxn.1_Missense_Mutation_p.R805Q|SH3PXD2A_uc010qqu.1_Missense_Mutation_p.R913Q	NM_014631	NP_055446	Q5TCZ1	SPD2A_HUMAN	SH3 multiple domains 1	998					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)														---	---	---	---
C10orf78	119392	broad.mit.edu	37	10	105883598	105883598	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105883598G>A	uc001kxu.2	+	3	275	c.262G>A	c.(262-264)GCA>ACA	p.A88T	C10orf78_uc001kxs.2_Missense_Mutation_p.A75T|C10orf78_uc001kxt.2_Missense_Mutation_p.A42T|C10orf78_uc001kxv.2_Missense_Mutation_p.A150T	NM_001002759	NP_001002759	Q86XK3	SFR1_HUMAN	hypothetical protein LOC119392 isoform a	88					double-strand break repair via homologous recombination	Swi5-Sfr1 complex	protein binding				0		Colorectal(252;0.102)|Breast(234;0.122)		Epithelial(162;1.31e-09)|all cancers(201;3.84e-08)|BRCA - Breast invasive adenocarcinoma(275;0.014)														---	---	---	---
ADRA2A	150	broad.mit.edu	37	10	112838219	112838219	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112838219G>A	uc001kzo.2	+	1	1430	c.465G>A	c.(463-465)GAG>GAA	p.E155E		NM_000681	NP_000672	P08913	ADA2A_HUMAN	alpha-2A-adrenergic receptor	140	Cytoplasmic (By similarity).				actin cytoskeleton organization|activation of MAPK activity by adrenergic receptor signaling pathway|activation of phospholipase C activity by adrenergic receptor signaling pathway|activation of protein kinase B activity|blood coagulation|cellular component movement|cellular response to hormone stimulus|energy reserve metabolic process|epidermal growth factor receptor transactivation by G-protein coupled receptor signaling pathway|glucose homeostasis|inhibition of adenylate cyclase activity by adrenergic receptor signaling pathway|intestinal absorption|negative regulation of adrenergic receptor signaling pathway|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of cAMP biosynthetic process|negative regulation of epinephrine secretion|negative regulation of insulin secretion involved in cellular response to glucose stimulus|negative regulation of lipid catabolic process|negative regulation of norepinephrine secretion|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of cytokine production|positive regulation of membrane protein ectodomain proteolysis|positive regulation of potassium ion transport|positive regulation of wound healing|Rho protein signal transduction	basolateral plasma membrane|cytoplasm|integral to plasma membrane|receptor complex	alpha-1B adrenergic receptor binding|alpha-2C adrenergic receptor binding|alpha2-adrenergic receptor activity|epinephrine binding|heterotrimeric G-protein binding|norepinephrine binding|protein heterodimerization activity|protein homodimerization activity|protein kinase binding|thioesterase binding				0		Breast(234;0.0735)|Lung NSC(174;0.238)		Epithelial(162;0.000316)|all cancers(201;0.00501)|BRCA - Breast invasive adenocarcinoma(275;0.118)	Amitriptyline(DB00321)|Amphetamine(DB00182)|Apraclonidine(DB00964)|Benzphetamine(DB00865)|Bethanidine(DB00217)|Brimonidine(DB00484)|Clonidine(DB00575)|Debrisoquin(DB04840)|Dexmedetomidine(DB00633)|Dipivefrin(DB00449)|Epinastine(DB00751)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Guanabenz(DB00629)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Guanfacine(DB01018)|Lofexidine(DB04948)|Methyldopa(DB00968)|Mianserin(DB06148)|Mirtazapine(DB00370)|Norepinephrine(DB00368)|Oxymetazoline(DB00935)|Phentolamine(DB00692)|Phenylpropanolamine(DB00397)|Pseudoephedrine(DB00852)|Tizanidine(DB00697)|Trazodone(DB00656)|Yohimbine(DB01392)													---	---	---	---
TCF7L2	6934	broad.mit.edu	37	10	114710645	114710645	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114710645G>A	uc001lae.3	+	1	637	c.130G>A	c.(130-132)GTC>ATC	p.V44I	TCF7L2_uc001lac.3_Missense_Mutation_p.V44I|TCF7L2_uc010qrk.1_Missense_Mutation_p.V44I|TCF7L2_uc010qrl.1_Missense_Mutation_p.V44I|TCF7L2_uc010qrm.1_Missense_Mutation_p.V44I|TCF7L2_uc010qrn.1_Missense_Mutation_p.V44I|TCF7L2_uc001lad.3_Missense_Mutation_p.V44I|TCF7L2_uc001lag.3_Missense_Mutation_p.V44I|TCF7L2_uc001laf.3_Missense_Mutation_p.V44I|TCF7L2_uc010qro.1_Missense_Mutation_p.V44I|TCF7L2_uc001lah.2_Missense_Mutation_p.V44I|TCF7L2_uc010qrp.1_Missense_Mutation_p.V44I|TCF7L2_uc010qrq.1_Missense_Mutation_p.V44I|TCF7L2_uc010qrr.1_5'Flank|TCF7L2_uc010qrs.1_5'Flank|TCF7L2_uc010qrt.1_5'Flank	NM_001146274	NP_001139746	Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 isoform 1	44	CTNNB1-binding (By similarity).				anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			large_intestine(3)|ovary(1)	4		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)														---	---	---	---
DCLRE1A	9937	broad.mit.edu	37	10	115602142	115602142	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115602142G>A	uc001law.2	-	6	3543	c.2625C>T	c.(2623-2625)GTC>GTT	p.V875V		NM_014881	NP_055696	Q6PJP8	DCR1A_HUMAN	DNA cross-link repair 1A	875					cell division|mitosis	nucleus	hydrolase activity			skin(2)	2				Epithelial(162;0.0157)|all cancers(201;0.0171)									Direct_reversal_of_damage|Other_identified_genes_with_known_or_suspected_DNA_repair_function					---	---	---	---
C10orf118	55088	broad.mit.edu	37	10	115922438	115922438	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115922438C>T	uc001lbb.1	-	2	1242	c.590G>A	c.(589-591)TGT>TAT	p.C197Y	C10orf118_uc001lbc.1_Missense_Mutation_p.C197Y|C10orf118_uc009xye.1_RNA|C10orf118_uc001lbd.2_Missense_Mutation_p.C197Y|C10orf118_uc001lbe.2_Missense_Mutation_p.C197Y	NM_018017	NP_060487	Q7Z3E2	CJ118_HUMAN	CTCL tumor antigen L14-2	197										ovary(2)	2		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0161)|all cancers(201;0.0397)														---	---	---	---
PNLIPRP1	5407	broad.mit.edu	37	10	118360647	118360647	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118360647G>A	uc001lco.1	+	10	1015	c.997G>A	c.(997-999)GCT>ACT	p.A333T	PNLIPRP1_uc001lcp.2_Missense_Mutation_p.A333T	NM_006229	NP_006220	P54315	LIPR1_HUMAN	pancreatic lipase-related protein 1 precursor	333					lipid metabolic process		calcium ion binding|triglyceride lipase activity			ovary(1)|breast(1)	2				all cancers(201;0.0161)														---	---	---	---
HSPA12A	259217	broad.mit.edu	37	10	118439082	118439082	+	Silent	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118439082G>T	uc001lct.2	-	10	1323	c.1218C>A	c.(1216-1218)CCC>CCA	p.P406P	HSPA12A_uc001lcu.2_Silent_p.P323P	NM_025015	NP_079291	O43301	HS12A_HUMAN	heat shock 70kDa protein 12A	406							ATP binding			ovary(1)	1				all cancers(201;0.0158)														---	---	---	---
SLC18A2	6571	broad.mit.edu	37	10	119029662	119029662	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119029662G>A	uc001ldd.1	+	14	1298	c.1267G>A	c.(1267-1269)GCC>ACC	p.A423T	SLC18A2_uc009xyy.1_Missense_Mutation_p.A220T	NM_003054	NP_003045	Q05940	VMAT2_HUMAN	solute carrier family 18 (vesicular monoamine),	423	Helical; (Potential).				neurotransmitter secretion	clathrin sculpted monoamine transport vesicle membrane|integral to plasma membrane|membrane fraction	monoamine transmembrane transporter activity				0		Colorectal(252;0.19)		all cancers(201;0.029)	Alseroxylon(DB00386)|Reserpine(DB00206)|Tetrabenazine(DB04844)													---	---	---	---
DMBT1	1755	broad.mit.edu	37	10	124350999	124350999	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124350999G>A	uc001lgk.1	+	19	2248	c.2142G>A	c.(2140-2142)ACG>ACA	p.T714T	DMBT1_uc001lgl.1_Silent_p.T704T|DMBT1_uc001lgm.1_Intron|DMBT1_uc009xzz.1_Silent_p.T714T|DMBT1_uc010qtx.1_Intron|DMBT1_uc009yaa.1_Intron	NM_007329	NP_015568	Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1 isoform b	714					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)																---	---	---	---
MKI67	4288	broad.mit.edu	37	10	129904364	129904364	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129904364C>A	uc001lke.2	-	13	5935	c.5740G>T	c.(5740-5742)GAG>TAG	p.E1914*	MKI67_uc001lkf.2_Nonsense_Mutation_p.E1554*|MKI67_uc009yav.1_Nonsense_Mutation_p.E1489*|MKI67_uc009yaw.1_Nonsense_Mutation_p.E1064*	NM_002417	NP_002408	P46013	KI67_HUMAN	antigen identified by monoclonal antibody Ki-67	1914	16 X 122 AA approximate repeats.|8.				cell proliferation	nucleolus	ATP binding|protein C-terminus binding			ovary(4)|central_nervous_system(2)|skin(1)	7		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)																---	---	---	---
B4GALNT4	338707	broad.mit.edu	37	11	380410	380410	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:380410G>A	uc001lpb.2	+	18	2843	c.2834G>A	c.(2833-2835)CGC>CAC	p.R945H		NM_178537	NP_848632	Q76KP1	B4GN4_HUMAN	beta	945	Lumenal (Potential).					Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			pancreas(1)	1		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
MUC5B	727897	broad.mit.edu	37	11	1251338	1251338	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1251338G>T	uc009ycr.1	+	27	3427	c.3301G>T	c.(3301-3303)GAC>TAC	p.D1101Y	MUC5B_uc009yct.1_Missense_Mutation_p.D442Y|MUC5B_uc001ltb.2_Missense_Mutation_p.D445Y|MUC5B_uc001lta.2_Missense_Mutation_p.D110Y	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	442	VWFD 2.				cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)														---	---	---	---
OR51A4	401666	broad.mit.edu	37	11	4967762	4967762	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4967762G>A	uc010qys.1	-	1	569	c.569C>T	c.(568-570)GCC>GTC	p.A190V		NM_001005329	NP_001005329	Q8NGJ6	O51A4_HUMAN	olfactory receptor, family 51, subfamily A,	190	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(1)	3		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)														---	---	---	---
OR52A4	390053	broad.mit.edu	37	11	5142402	5142402	+	Missense_Mutation	SNP	C	T	T	rs150996952	byFrequency;by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5142402C>T	uc001lzz.1	-	1	407	c.407G>A	c.(406-408)CGT>CAT	p.R136H	OR52A4_uc001maa.2_RNA	NM_001005222	NP_001005222			olfactory receptor, family 52, subfamily A,											ovary(2)	2		Medulloblastoma(188;0.0049)|all_neural(188;0.0442)|Breast(177;0.0675)		Epithelial(150;1.7e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.2)														---	---	---	---
OR51Q1	390061	broad.mit.edu	37	11	5443757	5443757	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5443757C>A	uc010qzd.1	+	1	327	c.327C>A	c.(325-327)TTC>TTA	p.F109L	HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Intron|OR51B5_uc001maq.1_Intron	NM_001004757	NP_001004757	Q8NH59	O51Q1_HUMAN	olfactory receptor, family 51, subfamily Q,	109	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.18e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
TRIM6-TRIM34	445372	broad.mit.edu	37	11	5624475	5624475	+	Splice_Site	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5624475G>T	uc001mbf.2	+	2	262	c.18_splice	c.e2-1	p.R6_splice	HBG2_uc001mak.1_Intron|TRIM6_uc009yeo.1_Splice_Site|TRIM6_uc010qzj.1_Intron|TRIM6_uc001mbc.1_Splice_Site|TRIM6_uc001mbe.2_Intron|TRIM6_uc010qzk.1_Intron|TRIM6_uc010qzl.1_Intron|TRIM6_uc001mbd.2_Splice_Site_p.R6_splice|TRIM6_uc001mbg.1_5'Flank|TRIM6_uc009yep.1_5'Flank	NM_001003819	NP_001003819			tripartite motif-containing 6 and tripartite							intracellular	zinc ion binding			ovary(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;1.01e-08)|BRCA - Breast invasive adenocarcinoma(625;0.145)														---	---	---	---
TRIM6-TRIM34	445372	broad.mit.edu	37	11	5624720	5624720	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5624720C>T	uc001mbf.2	+	2	506	c.262C>T	c.(262-264)CAG>TAG	p.Q88*	HBG2_uc001mak.1_Intron|TRIM6_uc009yeo.1_Nonsense_Mutation_p.Q60*|TRIM6_uc010qzj.1_Intron|TRIM6_uc001mbc.1_Nonsense_Mutation_p.Q60*|TRIM6_uc001mbe.2_Intron|TRIM6_uc010qzk.1_Intron|TRIM6_uc010qzl.1_Intron|TRIM6_uc001mbd.2_Nonsense_Mutation_p.Q88*|TRIM6_uc001mbg.1_5'Flank|TRIM6_uc009yep.1_5'Flank	NM_001003819	NP_001003819	B2RNG4	B2RNG4_HUMAN	tripartite motif-containing 6 and tripartite	88						intracellular	zinc ion binding			ovary(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;1.01e-08)|BRCA - Breast invasive adenocarcinoma(625;0.145)														---	---	---	---
OR52N5	390075	broad.mit.edu	37	11	5799447	5799447	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5799447G>A	uc010qzn.1	-	1	418	c.418C>T	c.(418-420)CGT>TGT	p.R140C	TRIM5_uc001mbq.1_Intron|TRIM22_uc009yet.1_Intron	NM_001001922	NP_001001922	Q8NH56	O52N5_HUMAN	olfactory receptor, family 52, subfamily N,	140	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.05e-11)|LUSC - Lung squamous cell carcinoma(625;0.112)|BRCA - Breast invasive adenocarcinoma(625;0.135)|Lung(200;0.195)														---	---	---	---
TRIM3	10612	broad.mit.edu	37	11	6477886	6477886	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6477886G>A	uc001mdh.2	-	7	1457	c.1070C>T	c.(1069-1071)ACA>ATA	p.T357I	TRIM3_uc001mdi.2_Missense_Mutation_p.T357I|TRIM3_uc010raj.1_Missense_Mutation_p.T238I|TRIM3_uc009yfd.2_Missense_Mutation_p.T357I|TRIM3_uc010rak.1_Missense_Mutation_p.T357I|TRIM3_uc001mdj.2_Missense_Mutation_p.T238I	NM_006458	NP_006449	O75382	TRIM3_HUMAN	tripartite motif-containing 3	357	Filamin.				nervous system development|protein transport	early endosome	protein C-terminus binding|zinc ion binding			central_nervous_system(2)|large_intestine(1)|ovary(1)|skin(1)	5		all_lung(207;9.97e-06)|Lung NSC(207;1.74e-05)|Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;9.34e-10)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.133)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
DCHS1	8642	broad.mit.edu	37	11	6655172	6655172	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6655172T>C	uc001mem.1	-	4	2476	c.2066A>G	c.(2065-2067)GAG>GGG	p.E689G		NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN	dachsous 1 precursor	689	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)														---	---	---	---
NLRP10	338322	broad.mit.edu	37	11	7981810	7981810	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7981810T>C	uc001mfv.1	-	2	1366	c.1349A>G	c.(1348-1350)AAC>AGC	p.N450S		NM_176821	NP_789791	Q86W26	NAL10_HUMAN	NLR family, pyrin domain containing 10	450	NACHT.						ATP binding			lung(4)|ovary(2)|pancreas(1)|kidney(1)|skin(1)	9				Epithelial(150;1.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)														---	---	---	---
ST5	6764	broad.mit.edu	37	11	8751527	8751527	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8751527T>C	uc001mgt.2	-	3	1496	c.1310A>G	c.(1309-1311)GAC>GGC	p.D437G	ST5_uc009yfr.2_Intron|ST5_uc001mgu.2_Intron|ST5_uc001mgv.2_Missense_Mutation_p.D437G|ST5_uc010rbq.1_Intron|ST5_uc001mgw.1_Missense_Mutation_p.D437G	NM_213618	NP_998783	P78524	ST5_HUMAN	suppression of tumorigenicity 5 isoform 1	437	Interaction with ABL1.				positive regulation of ERK1 and ERK2 cascade		protein binding			upper_aerodigestive_tract(1)	1				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)														---	---	---	---
SCUBE2	57758	broad.mit.edu	37	11	9088333	9088333	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9088333C>T	uc001mhh.1	-	6	751	c.671G>A	c.(670-672)TGC>TAC	p.C224Y	SCUBE2_uc001mhi.1_Missense_Mutation_p.C224Y|SCUBE2_uc001mhj.1_Missense_Mutation_p.C224Y	NM_020974	NP_066025	Q9NQ36	SCUB2_HUMAN	CEGP1 protein precursor	224	EGF-like 5 (Potential).					extracellular region	calcium ion binding			ovary(1)|skin(1)	2				all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)														---	---	---	---
SCUBE2	57758	broad.mit.edu	37	11	9096084	9096084	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9096084C>T	uc001mhh.1	-	4	541	c.461G>A	c.(460-462)TGC>TAC	p.C154Y	SCUBE2_uc001mhi.1_Missense_Mutation_p.C154Y|SCUBE2_uc001mhj.1_Missense_Mutation_p.C154Y	NM_020974	NP_066025	Q9NQ36	SCUB2_HUMAN	CEGP1 protein precursor	154	EGF-like 3; calcium-binding (Potential).					extracellular region	calcium ion binding			ovary(1)|skin(1)	2				all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)														---	---	---	---
SBF2	81846	broad.mit.edu	37	11	9874241	9874241	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9874241T>C	uc001mib.2	-	21	2730	c.2592A>G	c.(2590-2592)AGA>AGG	p.R864R	SBF2_uc001mif.3_Silent_p.R620R|uc001mig.2_Intron	NM_030962	NP_112224	Q86WG5	MTMRD_HUMAN	SET binding factor 2	864					myelination	cytoplasm|membrane	phosphatase activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)														---	---	---	---
TEAD1	7003	broad.mit.edu	37	11	12951777	12951777	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12951777A>G	uc001mkj.3	+	12	1691	c.1026A>G	c.(1024-1026)CCA>CCG	p.P342P	TEAD1_uc001mkk.3_Silent_p.P261P|TEAD1_uc009ygl.2_Silent_p.P178P	NM_021961	NP_068780	P28347	TEAD1_HUMAN	TEA domain family member 1	357	Transcriptional activation (Potential).				hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0				Epithelial(150;0.00223)|BRCA - Breast invasive adenocarcinoma(625;0.236)														---	---	---	---
ABCC8	6833	broad.mit.edu	37	11	17474667	17474667	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17474667T>C	uc001mnc.2	-	7	1301	c.1175A>G	c.(1174-1176)CAG>CGG	p.Q392R	ABCC8_uc010rcy.1_Missense_Mutation_p.Q391R	NM_000352	NP_000343	Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C, member 8	392	Cytoplasmic (By similarity).|ABC transmembrane type-1 1.				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)													---	---	---	---
NAV2	89797	broad.mit.edu	37	11	20075649	20075649	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20075649G>A	uc010rdm.1	+	19	4935	c.4574G>A	c.(4573-4575)CGC>CAC	p.R1525H	NAV2_uc001mpp.2_Missense_Mutation_p.R1438H|NAV2_uc001mpr.3_Missense_Mutation_p.R1502H|NAV2_uc001mpt.2_Missense_Mutation_p.R551H|NAV2_uc009yhx.2_Missense_Mutation_p.R566H|NAV2_uc009yhy.1_Missense_Mutation_p.R464H|NAV2_uc009yhz.2_Missense_Mutation_p.R147H|NAV2_uc001mpu.2_5'Flank	NM_145117	NP_660093	Q8IVL1	NAV2_HUMAN	neuron navigator 2 isoform 2	1525	Ser-rich.					nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6																		---	---	---	---
NELL1	4745	broad.mit.edu	37	11	20959379	20959379	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20959379T>G	uc001mqe.2	+	10	1198	c.1045T>G	c.(1045-1047)TTA>GTA	p.L349V	NELL1_uc001mqf.2_Missense_Mutation_p.L349V|NELL1_uc009yid.2_Missense_Mutation_p.L377V|NELL1_uc010rdo.1_Missense_Mutation_p.L292V|NELL1_uc010rdp.1_Missense_Mutation_p.L109V	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor	349	VWFC 2.				cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3																		---	---	---	---
FIBIN	387758	broad.mit.edu	37	11	27016668	27016668	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27016668A>G	uc001mrd.2	+	1	1041	c.595A>G	c.(595-597)ACC>GCC	p.T199A		NM_203371	NP_976249	Q8TAL6	FIBIN_HUMAN	fin bud initiation factor homolog precursor	199						extracellular region|Golgi apparatus					0																		---	---	---	---
WT1	7490	broad.mit.edu	37	11	32452089	32452089	+	Intron	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32452089T>C	uc001mtn.1	-						WT1_uc001mtl.1_5'UTR|WT1_uc001mtm.1_5'UTR|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				---	---	---	---
PAMR1	25891	broad.mit.edu	37	11	35513674	35513674	+	Missense_Mutation	SNP	C	A	A	rs139122111		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35513674C>A	uc001mwg.2	-	3	341	c.298G>T	c.(298-300)GGG>TGG	p.G100W	PAMR1_uc001mwf.2_Missense_Mutation_p.G100W|PAMR1_uc010rew.1_Missense_Mutation_p.G100W|PAMR1_uc010rex.1_Missense_Mutation_p.G60W	NM_001001991	NP_001001991	Q6UXH9	PAMR1_HUMAN	regeneration associated muscle protease isoform	100					proteolysis	extracellular region	serine-type endopeptidase activity			ovary(2)	2																		---	---	---	---
PRR5L	79899	broad.mit.edu	37	11	36472839	36472839	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36472839C>T	uc001mwo.3	+	8	1055	c.666C>T	c.(664-666)CTC>CTT	p.L222L	PRR5L_uc001mwp.2_Silent_p.L222L|PRR5L_uc009ykk.2_Silent_p.L94L|PRR5L_uc010rfc.1_Intron	NM_001160167	NP_001153639	Q6MZQ0	PRR5L_HUMAN	protor-2 isoform a	222										ovary(1)	1																		---	---	---	---
DGKZ	8525	broad.mit.edu	37	11	46393685	46393685	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46393685C>T	uc001ncn.1	+	11	1581	c.1456C>T	c.(1456-1458)CTG>TTG	p.L486L	DGKZ_uc001nch.1_Silent_p.L314L|DGKZ_uc010rgq.1_Silent_p.L241L|DGKZ_uc001ncj.1_Silent_p.L264L|DGKZ_uc010rgr.1_Silent_p.L263L|DGKZ_uc001nck.1_Silent_p.L76L|DGKZ_uc001ncl.2_Silent_p.L298L|DGKZ_uc001ncm.2_Silent_p.L297L|DGKZ_uc009yky.1_Silent_p.L298L|DGKZ_uc010rgs.1_Silent_p.L275L	NM_001105540	NP_001099010	Q13574	DGKZ_HUMAN	diacylglycerol kinase zeta isoform 4	486	DAGKc.|Mediates interaction with RASGRP1.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell migration|intracellular signal transduction|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of mitotic cell cycle|platelet activation	cytoplasm|lamellipodium|nucleus|plasma membrane	ATP binding|diacylglycerol kinase activity|diacylglycerol kinase activity|lipid kinase activity|metal ion binding|protein binding|protein C-terminus binding			pancreas(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(35;0.0259)|Lung(87;0.141)														---	---	---	---
AMBRA1	55626	broad.mit.edu	37	11	46563495	46563495	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46563495C>A	uc010rgu.1	-	7	2432	c.2072G>T	c.(2071-2073)AGG>ATG	p.R691M	AMBRA1_uc010rgt.1_Missense_Mutation_p.R257M|AMBRA1_uc009ylc.1_Missense_Mutation_p.R691I|AMBRA1_uc001ncu.1_Missense_Mutation_p.R601M|AMBRA1_uc001ncv.2_Missense_Mutation_p.R601I|AMBRA1_uc001ncw.2_Missense_Mutation_p.R601I|AMBRA1_uc001ncx.2_Missense_Mutation_p.R691M	NM_017749	NP_060219	Q9C0C7	AMRA1_HUMAN	activating molecule in beclin-1-regulated	691					autophagy|cell differentiation|nervous system development	autophagic vacuole|cytoplasmic vesicle				large_intestine(1)|ovary(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)														---	---	---	---
CKAP5	9793	broad.mit.edu	37	11	46783572	46783572	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46783572T>C	uc001ndi.1	-	32	4309	c.4199A>G	c.(4198-4200)CAG>CGG	p.Q1400R	CKAP5_uc009ylg.1_Missense_Mutation_p.Q1286R|CKAP5_uc001ndj.1_Missense_Mutation_p.Q1400R|CKAP5_uc001ndh.1_Missense_Mutation_p.Q329R	NM_001008938	NP_001008938	Q14008	CKAP5_HUMAN	colonic and hepatic tumor over-expressed protein	1400					cell division|centrosome organization|establishment or maintenance of microtubule cytoskeleton polarity|G2/M transition of mitotic cell cycle|mitotic prometaphase|RNA transport|spindle organization	centrosome|cytosol	protein binding|protein binding			ovary(1)|skin(1)	2																		---	---	---	---
DDB2	1643	broad.mit.edu	37	11	47256937	47256937	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47256937C>T	uc001neb.2	+	7	1192	c.997C>T	c.(997-999)CAC>TAC	p.H333Y	DDB2_uc001nec.2_RNA|DDB2_uc009yli.1_Missense_Mutation_p.H269Y|DDB2_uc001ned.2_RNA|DDB2_uc001nee.2_Intron|DDB2_uc001nef.2_Intron|DDB2_uc001neg.2_Missense_Mutation_p.H192Y|DDB2_uc001neh.2_RNA	NM_000107	NP_000098	Q92466	DDB2_HUMAN	damage-specific DNA binding protein 2	333					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	47510486	47510486	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47510486C>T	uc001nfl.2	-	1	91	c.81G>A	c.(79-81)TGG>TGA	p.W27*	CELF1_uc001nfm.2_Nonsense_Mutation_p.W27*|CELF1_uc001nfn.2_Nonsense_Mutation_p.W27*|CELF1_uc001nfo.1_Nonsense_Mutation_p.W54*|CELF1_uc010rhm.1_Nonsense_Mutation_p.W27*|CELF1_uc001nfp.2_Nonsense_Mutation_p.W54*|CELF1_uc001nfq.1_Nonsense_Mutation_p.W27*|CELF1_uc001nfr.1_Nonsense_Mutation_p.W27*	NM_001025596	NP_001020767	Q92879	CELF1_HUMAN	CUG triplet repeat, RNA-binding protein 1	27	RRM 1.				embryo development|mRNA splice site selection|regulation of RNA splicing|RNA interference	cytoplasm|nucleus|ribonucleoprotein complex	BRE binding|mRNA binding|nucleotide binding|translation repressor activity, nucleic acid binding			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
FNBP4	23360	broad.mit.edu	37	11	47774629	47774629	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47774629T>C	uc009ylv.2	-	4	629	c.476A>G	c.(475-477)CAG>CGG	p.Q159R	FNBP4_uc001ngj.2_Missense_Mutation_p.Q66R|FNBP4_uc001ngl.2_RNA	NM_015308	NP_056123	Q8N3X1	FNBP4_HUMAN	formin binding protein 4	159										ovary(1)	1																		---	---	---	---
OR4A15	81328	broad.mit.edu	37	11	55136098	55136098	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55136098G>T	uc010rif.1	+	1	739	c.739G>T	c.(739-741)GGG>TGG	p.G247W		NM_001005275	NP_001005275	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A,	247	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2																		---	---	---	---
OR4C16	219428	broad.mit.edu	37	11	55340505	55340505	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55340505G>A	uc010rih.1	+	1	902	c.902G>A	c.(901-903)AGC>AAC	p.S301N		NM_001004701	NP_001004701	Q8NGL9	OR4CG_HUMAN	olfactory receptor, family 4, subfamily C,	301	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2		all_epithelial(135;0.0748)																---	---	---	---
OR8H2	390151	broad.mit.edu	37	11	55872630	55872630	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55872630A>C	uc010riy.1	+	1	112	c.112A>C	c.(112-114)ATT>CTT	p.I38L		NM_001005200	NP_001005200	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H,	38	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2	Esophageal squamous(21;0.00693)														HNSCC(53;0.14)			---	---	---	---
OR5B2	390190	broad.mit.edu	37	11	58190721	58190721	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58190721G>A	uc010rkg.1	-	1	14	c.14C>T	c.(13-15)ACG>ATG	p.T5M		NM_001005566	NP_001005566	Q96R09	OR5B2_HUMAN	olfactory receptor, family 5, subfamily B,	5	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	3	Esophageal squamous(5;0.0027)	Breast(21;0.0778)																---	---	---	---
LPXN	9404	broad.mit.edu	37	11	58322419	58322419	+	Intron	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58322419G>A	uc001nmw.2	-						LPXN_uc009ymp.2_Intron|LPXN_uc010rkj.1_Intron|LPXN_uc010rkk.1_Intron	NM_004811	NP_004802			leupaxin isoform 2						cell adhesion|protein complex assembly|signal transduction	cytoplasm	zinc ion binding			ovary(1)	1		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)																---	---	---	---
MPEG1	219972	broad.mit.edu	37	11	58979729	58979729	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58979729G>T	uc001nnu.3	-	1	766	c.610C>A	c.(610-612)CAC>AAC	p.H204N		NM_001039396	NP_001034485	Q2M385	MPEG1_HUMAN	macrophage expressed gene 1 precursor	204	MACPF.|Extracellular (Potential).					integral to membrane				ovary(1)|skin(1)	2		all_epithelial(135;0.125)																---	---	---	---
MS4A6A	64231	broad.mit.edu	37	11	59949148	59949148	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59949148A>C	uc001nor.2	-	2	291	c.53T>G	c.(52-54)GTC>GGC	p.V18G	MS4A6A_uc001noq.2_Missense_Mutation_p.V18G|MS4A6A_uc001nos.3_Missense_Mutation_p.V46G|MS4A6A_uc009ymv.2_Missense_Mutation_p.V18G|MS4A6A_uc001not.2_Missense_Mutation_p.V18G|MS4A6A_uc010rla.1_Missense_Mutation_p.V46G|MS4A6A_uc010rlb.1_Missense_Mutation_p.V18G	NM_152852	NP_690591	Q9H2W1	M4A6A_HUMAN	membrane-spanning 4-domains, subfamily A, member	18	Cytoplasmic (Potential).					integral to membrane	receptor activity				0																		---	---	---	---
MS4A13	503497	broad.mit.edu	37	11	60292773	60292773	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60292773G>A	uc001nps.2	+	5	603	c.280G>A	c.(280-282)GTG>ATG	p.V94M	MS4A13_uc009ync.2_Intron|MS4A13_uc009ynd.2_Intron	NM_001012417	NP_001012417	Q5J8X5	M4A13_HUMAN	membrane-spanning 4-domains, subfamily A, member	94						integral to membrane					0																		---	---	---	---
PRPF19	27339	broad.mit.edu	37	11	60665431	60665431	+	Intron	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60665431A>G	uc001nqf.2	-							NM_014502	NP_055317			PRP19/PSO4 pre-mRNA processing factor 19						DNA repair|protein polyubiquitination|spliceosome assembly	catalytic step 2 spliceosome|nuclear speck|spindle|ubiquitin ligase complex	DNA binding|identical protein binding|ubiquitin-ubiquitin ligase activity			ovary(1)	1																		---	---	---	---
TMEM132A	54972	broad.mit.edu	37	11	60703810	60703810	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60703810G>A	uc001nqj.2	+	11	2696	c.2503G>A	c.(2503-2505)GAG>AAG	p.E835K	TMEM132A_uc001nqi.2_Missense_Mutation_p.E836K|TMEM132A_uc001nqm.2_Missense_Mutation_p.E45K	NM_178031	NP_821174	Q24JP5	T132A_HUMAN	transmembrane protein 132A isoform b	835	Glu-rich.|Binds to HSPA5/GRP78 (By similarity).|Confers cellular localization similar to full-length form (By similarity).|Extracellular (Potential).					endoplasmic reticulum membrane|Golgi membrane|integral to membrane				skin(1)	1																		---	---	---	---
STX5	6811	broad.mit.edu	37	11	62575011	62575011	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62575011C>T	uc001nvh.2	-	11	1152	c.998G>A	c.(997-999)CGG>CAG	p.R333Q	NXF1_uc001nvf.1_5'Flank|NXF1_uc001nvg.1_5'Flank|NXF1_uc009yog.1_5'Flank|NXF1_uc010rmh.1_5'Flank|STX5_uc010rmi.1_Missense_Mutation_p.R237Q|STX5_uc009yoh.2_RNA|STX5_uc001nvi.2_Missense_Mutation_p.R279Q|STX5_uc010rmj.1_3'UTR|STX5_uc001nvj.2_Missense_Mutation_p.R148Q	NM_003164	NP_003155	Q13190	STX5_HUMAN	syntaxin 5	333	Cytoplasmic (Potential).				intracellular protein transport|retrograde transport, endosome to Golgi|vesicle targeting	ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane|nucleus|SNARE complex	protein N-terminus binding|SNAP receptor activity			ovary(1)|breast(1)	2																		---	---	---	---
ATL3	25923	broad.mit.edu	37	11	63398891	63398891	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63398891T>C	uc001nxk.1	-	12	1436	c.1160A>G	c.(1159-1161)CAC>CGC	p.H387R	ATL3_uc010rms.1_Missense_Mutation_p.H369R|ATL3_uc010rmr.1_Missense_Mutation_p.H45R	NM_015459	NP_056274	Q6DD88	ATLA3_HUMAN	atlastin 3	387	Cytoplasmic.				endoplasmic reticulum organization|Golgi organization|protein homooligomerization	endoplasmic reticulum membrane|integral to membrane	GTP binding|GTPase activity|identical protein binding			pancreas(1)	1																		---	---	---	---
SLC22A12	116085	broad.mit.edu	37	11	64361023	64361023	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64361023G>A	uc001oam.1	+	3	1400	c.653G>A	c.(652-654)GGC>GAC	p.G218D	SLC22A12_uc009ypr.1_Missense_Mutation_p.G218D|SLC22A12_uc001oal.1_Intron|SLC22A12_uc009yps.1_Intron|SLC22A12_uc001oan.1_Intron|SLC22A12_uc009ypt.2_Missense_Mutation_p.G36D	NM_144585	NP_653186	Q96S37	S22AC_HUMAN	urate anion exchanger 1 isoform a	218					cellular homeostasis|response to drug|urate metabolic process	apical plasma membrane|brush border membrane|integral to membrane	PDZ domain binding|urate transmembrane transporter activity			ovary(1)	1																		---	---	---	---
ATG2A	23130	broad.mit.edu	37	11	64665432	64665432	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64665432G>A	uc001obx.2	-	35	4988	c.4873C>T	c.(4873-4875)CGA>TGA	p.R1625*	ATG2A_uc001obw.2_Nonsense_Mutation_p.R390*	NM_015104	NP_055919	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	1625							protein binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
SPDYC	387778	broad.mit.edu	37	11	64939751	64939751	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64939751G>A	uc010rnz.1	+	4	293	c.293G>A	c.(292-294)CGC>CAC	p.R98H		NM_001008778	NP_001008778	Q5MJ68	SPDYC_HUMAN	speedy C	98	Speedy/Ringo box; Required for CDK- binding (By similarity).				cell cycle	nucleus	protein kinase binding				0																		---	---	---	---
TIGD3	220359	broad.mit.edu	37	11	65124515	65124515	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65124515A>G	uc001odo.3	+	2	1399	c.1236A>G	c.(1234-1236)ATA>ATG	p.I412M		NM_145719	NP_663771	Q6B0B8	TIGD3_HUMAN	tigger transposable element derived 3	412					regulation of transcription, DNA-dependent	chromosome, centromeric region|nucleus	DNA binding				0																		---	---	---	---
CTSW	1521	broad.mit.edu	37	11	65651098	65651098	+	3'UTR	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65651098G>T	uc001ogc.1	+	10					CTSW_uc001ogb.1_3'UTR	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)														---	---	---	---
NPAS4	266743	broad.mit.edu	37	11	66189916	66189916	+	Intron	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66189916C>A	uc001ohx.1	+						NPAS4_uc010rpc.1_Intron	NM_178864	NP_849195			neuronal PAS domain protein 4						transcription, DNA-dependent		DNA binding|signal transducer activity				0																		---	---	---	---
BBS1	582	broad.mit.edu	37	11	66282076	66282076	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66282076C>A	uc001oij.1	+	4	371	c.359C>A	c.(358-360)CCC>CAC	p.P120H	BBS1_uc001oii.1_Missense_Mutation_p.P157H|BBS1_uc010rpf.1_RNA|BBS1_uc010rpg.1_Missense_Mutation_p.P120H|BBS1_uc001oik.1_Missense_Mutation_p.P44H|BBS1_uc001oil.1_Missense_Mutation_p.P120H	NM_024649	NP_078925	Q8NFJ9	BBS1_HUMAN	Bardet-Biedl syndrome 1	120					nonmotile primary cilium assembly|photoreceptor cell maintenance|response to stimulus|retina homeostasis	BBSome|cilium membrane|cytoplasm	protein binding			ovary(1)	1														Bardet-Biedl_syndrome				---	---	---	---
SSH3	54961	broad.mit.edu	37	11	67072438	67072438	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67072438T>A	uc001okj.2	+	3	477	c.299T>A	c.(298-300)CTC>CAC	p.L100H	SSH3_uc001okk.2_RNA|SSH3_uc001okl.2_5'UTR	NM_017857	NP_060327	Q8TE77	SSH3_HUMAN	slingshot homolog 3	100					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)															---	---	---	---
NDUFS8	4728	broad.mit.edu	37	11	67804062	67804062	+	3'UTR	SNP	G	A	A	rs34470466		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67804062G>A	uc001onc.2	+	7					NDUFS8_uc009ysb.1_RNA|NDUFS8_uc009ysc.1_3'UTR|TCIRG1_uc001ond.1_5'Flank|TCIRG1_uc001one.2_5'Flank	NM_002496	NP_002487			NADH dehydrogenase ubiquinone Fe-S 8 precursor						mitochondrial electron transport, NADH to ubiquinone|mitochondrial respiratory chain complex I assembly|response to oxidative stress|transport	mitochondrial respiratory chain complex I	4 iron, 4 sulfur cluster binding|electron carrier activity|metal ion binding|NADH dehydrogenase (ubiquinone) activity			skin(1)	1					NADH(DB00157)													---	---	---	---
LRP5	4041	broad.mit.edu	37	11	68191163	68191163	+	Silent	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68191163A>C	uc001ont.2	+	14	3309	c.3234A>C	c.(3232-3234)CGA>CGC	p.R1078R	LRP5_uc009ysg.2_Silent_p.R488R	NM_002335	NP_002326	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein	1078	LDL-receptor class B 17.|Beta-propeller 4.|Extracellular (Potential).				adipose tissue development|bone marrow development|bone morphogenesis|canonical Wnt receptor signaling pathway|cholesterol homeostasis|endocytosis|glucose catabolic process|negative regulation of osteoblast differentiation|negative regulation of protein serine/threonine kinase activity|positive regulation of fat cell differentiation|positive regulation of mesenchymal cell proliferation|positive regulation of mitosis|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of canonical Wnt receptor signaling pathway|retina morphogenesis in camera-type eye|retinal blood vessel morphogenesis|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	endoplasmic reticulum|integral to membrane|plasma membrane|receptor complex	protein binding|receptor activity			lung(2)|skin(2)|ovary(1)|pancreas(1)|breast(1)	7																		---	---	---	---
PPFIA1	8500	broad.mit.edu	37	11	70178133	70178133	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70178133T>C	uc001opo.2	+	9	1343	c.1145T>C	c.(1144-1146)CTG>CCG	p.L382P	PPFIA1_uc001opn.1_Missense_Mutation_p.L382P|PPFIA1_uc001opp.2_RNA|PPFIA1_uc001opq.1_RNA	NM_003626	NP_003617	Q13136	LIPA1_HUMAN	PTPRF interacting protein alpha 1 isoform b	382	Potential.				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)															---	---	---	---
NADSYN1	55191	broad.mit.edu	37	11	71195454	71195454	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71195454A>G	uc001oqn.2	+	15	1542	c.1416A>G	c.(1414-1416)GGA>GGG	p.G472G	NADSYN1_uc001oqo.2_Silent_p.G212G|NADSYN1_uc001oqp.2_Silent_p.G101G	NM_018161	NP_060631	Q6IA69	NADE_HUMAN	NAD synthetase 1	472	Ligase (By similarity).				NAD biosynthetic process|water-soluble vitamin metabolic process	cytosol	ATP binding|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds|NAD+ synthase (glutamine-hydrolyzing) activity|protein binding			ovary(2)	2					L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)													---	---	---	---
SERPINH1	871	broad.mit.edu	37	11	75283093	75283093	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75283093C>T	uc001owr.2	+	5	1451	c.1222C>T	c.(1222-1224)CGG>TGG	p.R408W	SERPINH1_uc009yug.2_Missense_Mutation_p.R408W|SERPINH1_uc001ows.2_Missense_Mutation_p.R408W|SERPINH1_uc001owt.2_Missense_Mutation_p.R191W	NM_001235	NP_001226	P50454	SERPH_HUMAN	serine (or cysteine) proteinase inhibitor, clade	408					regulation of proteolysis|response to unfolded protein	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	collagen binding|serine-type endopeptidase inhibitor activity			ovary(2)	2	Ovarian(111;0.11)																	---	---	---	---
RSF1	51773	broad.mit.edu	37	11	77436752	77436752	+	Intron	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77436752A>G	uc001oyn.2	-							NM_016578	NP_057662			remodeling and spacing factor 1						CenH3-containing nucleosome assembly at centromere|negative regulation of DNA binding|negative regulation of transcription, DNA-dependent|nucleosome positioning|positive regulation of transcription, DNA-dependent|positive regulation of viral transcription|transcription initiation, DNA-dependent	RSF complex	histone binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(2)	4	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)															---	---	---	---
INTS4	92105	broad.mit.edu	37	11	77649810	77649810	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77649810C>T	uc001oys.2	-	10	1080	c.1052G>A	c.(1051-1053)GGC>GAC	p.G351D	INTS4_uc001oyt.2_RNA|INTS4_uc001oyu.1_Missense_Mutation_p.G351D	NM_033547	NP_291025	Q96HW7	INT4_HUMAN	integrator complex subunit 4	351					snRNA processing	integrator complex	protein binding			ovary(2)	2	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)															---	---	---	---
ODZ4	26011	broad.mit.edu	37	11	78369636	78369636	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78369636T>C	uc001ozl.3	-	34	8240	c.7777A>G	c.(7777-7779)AGG>GGG	p.R2593G	ODZ4_uc001ozk.3_Missense_Mutation_p.R818G|ODZ4_uc009yvb.1_Intron	NM_001098816	NP_001092286	Q6N022	TEN4_HUMAN	odz, odd Oz/ten-m homolog 4	2593	Extracellular (Potential).				signal transduction	integral to membrane				ovary(2)|pancreas(2)	4																		---	---	---	---
SYTL2	54843	broad.mit.edu	37	11	85468669	85468669	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85468669T>C	uc010rth.1	-	1	376	c.100A>G	c.(100-102)AGA>GGA	p.R34G	SYTL2_uc010rtg.1_Missense_Mutation_p.R34G|SYTL2_uc010rti.1_Missense_Mutation_p.R34G|SYTL2_uc010rtj.1_Intron|SYTL2_uc001pbf.3_Missense_Mutation_p.R34G	NM_001162951	NP_001156423	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2 isoform g	34	RabBD.				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)														---	---	---	---
PRSS23	11098	broad.mit.edu	37	11	86519362	86519362	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86519362G>A	uc001pcb.2	+	2	893	c.677G>A	c.(676-678)CGC>CAC	p.R226H	PRSS23_uc001pcc.1_Intron|PRSS23_uc010rts.1_Missense_Mutation_p.R194H	NM_007173	NP_009104	O95084	PRS23_HUMAN	protease, serine, 23 precursor	226					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)																---	---	---	---
GRM5	2915	broad.mit.edu	37	11	88300414	88300414	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88300414C>T	uc001pcq.2	-	7	2637	c.2437G>A	c.(2437-2439)GCC>ACC	p.A813T	GRM5_uc009yvm.2_Missense_Mutation_p.A813T	NM_001143831	NP_001137303	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5 isoform a	813	Helical; Name=7; (Potential).				activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			central_nervous_system(4)|ovary(2)|lung(2)|breast(1)	9		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)													---	---	---	---
MED17	9440	broad.mit.edu	37	11	93528224	93528224	+	Missense_Mutation	SNP	C	A	A	rs148342933		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93528224C>A	uc001pem.3	+	6	1285	c.1010C>A	c.(1009-1011)CCG>CAG	p.P337Q		NM_004268	NP_004259	Q9NVC6	MED17_HUMAN	mediator complex subunit 17	337					androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex|transcription factor complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)																---	---	---	---
MAML2	84441	broad.mit.edu	37	11	95825852	95825852	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95825852C>T	uc001pfw.1	-	2	2628	c.1343G>A	c.(1342-1344)CGG>CAG	p.R448Q		NM_032427	NP_115803	Q8IZL2	MAML2_HUMAN	mastermind-like 2	448					Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity		CRTC1/MAML2(516)|CRTC3/MAML2(26)	salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1)	546		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)						T	MECT1|CRTC3	salivary gland mucoepidermoid								---	---	---	---
ZC3H12C	85463	broad.mit.edu	37	11	110035921	110035921	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110035921C>T	uc009yxw.2	+	6	2162	c.2111C>T	c.(2110-2112)CCG>CTG	p.P704L	ZC3H12C_uc010rwc.1_Missense_Mutation_p.P705L|ZC3H12C_uc010rwd.1_Missense_Mutation_p.P705L|ZC3H12C_uc001pkr.3_Missense_Mutation_p.P673L	NM_033390	NP_203748	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	704							endonuclease activity|nucleic acid binding|zinc ion binding				0		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)														---	---	---	---
DLAT	1737	broad.mit.edu	37	11	111930640	111930640	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111930640G>T	uc001pmo.2	+	12	2187	c.1528G>T	c.(1528-1530)GAT>TAT	p.D510Y	DLAT_uc009yyk.1_Missense_Mutation_p.D405Y|DLAT_uc010rwr.1_Missense_Mutation_p.D383Y	NM_001931	NP_001922	P10515	ODP2_HUMAN	dihydrolipoamide S-acetyltransferase precursor	510	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)													---	---	---	---
PIH1D2	120379	broad.mit.edu	37	11	111943818	111943818	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111943818A>G	uc001pmq.3	-	2	163	c.81T>C	c.(79-81)CCT>CCC	p.P27P	PIH1D2_uc009yyl.2_Silent_p.P27P|PIH1D2_uc001pmp.3_Silent_p.P27P|PIH1D2_uc010rws.1_Silent_p.P27P|C11orf57_uc001pmu.2_5'Flank|C11orf57_uc001pmw.3_5'Flank|C11orf57_uc001pmt.3_5'Flank|C11orf57_uc001pmr.3_5'Flank|C11orf57_uc001pmv.3_5'Flank|C11orf57_uc001pms.3_5'Flank	NM_138789	NP_620144	Q8WWB5	PIHD2_HUMAN	PIH1 domain containing 2 isoform 1	27										ovary(1)	1		all_cancers(61;1.09e-14)|all_epithelial(67;7.64e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;3.19e-07)|BRCA - Breast invasive adenocarcinoma(274;6.17e-07)|all cancers(92;6.18e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0508)														---	---	---	---
AMICA1	120425	broad.mit.edu	37	11	118081198	118081198	+	Intron	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118081198G>A	uc001psk.2	-						AMICA1_uc001psh.2_Intron|AMICA1_uc009yzw.1_Intron|AMICA1_uc001psi.2_Intron|AMICA1_uc001psj.2_Intron|AMICA1_uc010rxw.1_Intron|AMICA1_uc010rxx.1_Intron|AMICA1_uc001psl.1_Intron	NM_001098526	NP_001091996			adhesion molecule, interacts with CXADR antigen						blood coagulation|cell adhesion|leukocyte migration|regulation of immune response	cell junction|integral to membrane				ovary(1)	1	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)														---	---	---	---
MLL	4297	broad.mit.edu	37	11	118374587	118374587	+	Silent	SNP	C	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118374587C>G	uc001pta.2	+	27	7994	c.7971C>G	c.(7969-7971)GGC>GGG	p.G2657G	MLL_uc001ptb.2_Silent_p.G2660G	NM_005933	NP_005924	Q03164	MLL1_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	2657					apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter	MLL1 complex	AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding			lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1)	25	all_hematologic(175;0.046)	all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244)		OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144)				T|O	MLL|MLLT1|MLLT2|MLLT3|MLLT4|MLLT7|MLLT10|MLLT6|ELL|EPS15|AF1Q|CREBBP|SH3GL1|FNBP1|PNUTL1|MSF|GPHN|GMPS|SSH3BP1|ARHGEF12|GAS7|FOXO3A|LAF4|LCX|SEPT6|LPP|CBFA2T1|GRAF|EP300|PICALM|HEAB	AML|ALL								---	---	---	---
HYOU1	10525	broad.mit.edu	37	11	118926784	118926784	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118926784C>A	uc001puu.2	-	2	282	c.89G>T	c.(88-90)AGT>ATT	p.S30I	HYOU1_uc001put.2_5'Flank|HYOU1_uc010ryu.1_Missense_Mutation_p.S50I|HYOU1_uc010ryv.1_Intron|HYOU1_uc001pux.3_Missense_Mutation_p.S30I|HYOU1_uc010ryw.1_RNA|HYOU1_uc001puw.1_Missense_Mutation_p.S30I	NM_006389	NP_006380	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1 precursor	30						endoplasmic reticulum lumen	ATP binding|protein binding				0	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.78e-05)												OREG0021394	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SORL1	6653	broad.mit.edu	37	11	121445010	121445010	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121445010C>A	uc001pxx.2	+	24	3478	c.3398C>A	c.(3397-3399)CCA>CAA	p.P1133Q	SORL1_uc010rzp.1_5'Flank	NM_003105	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor containing LDLR class	1133	Extracellular (Potential).|LDL-receptor class A 2.				cholesterol metabolic process|lipid transport|receptor-mediated endocytosis	integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|transmembrane receptor activity			ovary(5)|breast(4)|large_intestine(2)|skin(2)|central_nervous_system(1)|pancreas(1)	15		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)														---	---	---	---
GRAMD1B	57476	broad.mit.edu	37	11	123483474	123483474	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123483474C>T	uc001pyx.2	+	14	1825	c.1496C>T	c.(1495-1497)TCC>TTC	p.S499F	GRAMD1B_uc001pyw.2_Missense_Mutation_p.S506F|GRAMD1B_uc010rzw.1_Missense_Mutation_p.S459F|GRAMD1B_uc010rzx.1_Missense_Mutation_p.S459F|GRAMD1B_uc001pyy.2_Missense_Mutation_p.S190F	NM_020716	NP_065767	Q3KR37	GRM1B_HUMAN	GRAM domain containing 1B	499						integral to membrane				ovary(1)	1		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)														---	---	---	---
ETS1	2113	broad.mit.edu	37	11	128350333	128350333	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128350333G>A	uc010sbs.1	-	6	1060	c.744C>T	c.(742-744)GGC>GGT	p.G248G	ETS1_uc001qej.2_Silent_p.G292G|ETS1_uc009zch.2_Silent_p.G32G|ETS1_uc009zcg.2_Silent_p.G248G	NM_005238	NP_005229	P14921	ETS1_HUMAN	v-ets erythroblastosis virus E26 oncogene	248					cell motility|immune response|induction of apoptosis|negative regulation of cell cycle|negative regulation of cell cycle|negative regulation of cell proliferation|PML body organization|positive regulation of cellular component movement|positive regulation of erythrocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|response to antibiotic|transcription from RNA polymerase II promoter	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			lung(4)|central_nervous_system(1)|pleura(1)	6	all_hematologic(175;0.0537)	Lung NSC(97;0.000542)|all_lung(97;0.000665)|Breast(109;0.00765)|all_neural(223;0.0351)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.47e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0174)|LUSC - Lung squamous cell carcinoma(976;0.0815)|Lung(307;0.0833)														---	---	---	---
PRDM10	56980	broad.mit.edu	37	11	129784852	129784852	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129784852A>G	uc001qfm.2	-	18	2832	c.2600T>C	c.(2599-2601)ATA>ACA	p.I867T	PRDM10_uc001qfj.2_Missense_Mutation_p.I781T|PRDM10_uc001qfk.2_Missense_Mutation_p.I777T|PRDM10_uc001qfl.2_Missense_Mutation_p.I781T|PRDM10_uc010sbx.1_Missense_Mutation_p.I777T|PRDM10_uc001qfn.2_Missense_Mutation_p.I863T|PRDM10_uc009zcs.1_Missense_Mutation_p.I50T	NM_020228	NP_064613	Q9NQV6	PRD10_HUMAN	PR domain containing 10 isoform 1	867	Thr-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)														---	---	---	---
ADAMTS15	170689	broad.mit.edu	37	11	130343003	130343003	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130343003C>T	uc010scd.1	+	8	2140	c.2140C>T	c.(2140-2142)CGC>TGC	p.R714C		NM_139055	NP_620686	Q8TE58	ATS15_HUMAN	a disintegrin-like and metalloprotease	714	Spacer.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(2)|pancreas(1)|lung(1)|skin(1)	5	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;0.0631)|Lung(977;0.215)														---	---	---	---
GLB1L2	89944	broad.mit.edu	37	11	134226264	134226264	+	Missense_Mutation	SNP	G	A	A	rs77130779		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134226264G>A	uc001qhp.2	+	6	816	c.628G>A	c.(628-630)GCA>ACA	p.A210T	GLB1L2_uc009zdg.1_RNA	NM_138342	NP_612351	Q8IW92	GLBL2_HUMAN	galactosidase, beta 1-like 2 precursor	210					carbohydrate metabolic process	extracellular region	cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			ovary(1)|pancreas(1)|skin(1)	3	all_hematologic(175;0.127)	all_cancers(12;2.85e-18)|all_epithelial(12;1.21e-12)|all_lung(97;0.000276)|Lung NSC(97;0.000518)|Breast(109;0.00122)|Medulloblastoma(222;0.0399)|all_neural(223;0.0412)|Esophageal squamous(93;0.0844)		Epithelial(10;1.37e-11)|all cancers(11;2.2e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000885)|Lung(977;0.223)														---	---	---	---
WNK1	65125	broad.mit.edu	37	12	1005549	1005549	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1005549A>G	uc001qio.3	+	24	6403	c.5896A>G	c.(5896-5898)AAG>GAG	p.K1966E	WNK1_uc001qip.3_Missense_Mutation_p.K1718E|WNK1_uc001qir.3_Missense_Mutation_p.K1139E	NM_018979	NP_061852	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	1966					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)															---	---	---	---
ERC1	23085	broad.mit.edu	37	12	1299217	1299217	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1299217A>G	uc001qjb.2	+	12	2591	c.2350A>G	c.(2350-2352)AGG>GGG	p.R784G	ERC1_uc001qiz.2_RNA|ERC1_uc001qjc.2_Missense_Mutation_p.R756G|ERC1_uc001qja.2_RNA|ERC1_uc001qjd.2_RNA|ERC1_uc001qjf.2_Missense_Mutation_p.R784G|ERC1_uc010sdv.1_Missense_Mutation_p.S532G|ERC1_uc009zdp.2_Missense_Mutation_p.R424G|ERC1_uc001qje.2_RNA	NM_178040	NP_829884	Q8IUD2	RB6I2_HUMAN	RAB6-interacting protein 2 isoform epsilon	784	Potential.				I-kappaB phosphorylation|multicellular organismal development|positive regulation of anti-apoptosis|positive regulation of NF-kappaB transcription factor activity|protein transport	Golgi membrane|IkappaB kinase complex|presynaptic membrane	leucine zipper domain binding			ovary(2)|lung(2)|breast(1)	5	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)															---	---	---	---
ERC1	23085	broad.mit.edu	37	12	1345988	1345988	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1345988T>C	uc001qjb.2	+	13	2646	c.2405T>C	c.(2404-2406)GTG>GCG	p.V802A	ERC1_uc001qiz.2_RNA|ERC1_uc001qjc.2_Missense_Mutation_p.V774A|ERC1_uc001qja.2_RNA|ERC1_uc001qjd.2_RNA|ERC1_uc001qjf.2_Missense_Mutation_p.V802A|ERC1_uc010sdv.1_Missense_Mutation_p.V554A|ERC1_uc009zdp.2_Missense_Mutation_p.V442A|ERC1_uc001qje.2_RNA	NM_178040	NP_829884	Q8IUD2	RB6I2_HUMAN	RAB6-interacting protein 2 isoform epsilon	802	Potential.				I-kappaB phosphorylation|multicellular organismal development|positive regulation of anti-apoptosis|positive regulation of NF-kappaB transcription factor activity|protein transport	Golgi membrane|IkappaB kinase complex|presynaptic membrane	leucine zipper domain binding			ovary(2)|lung(2)|breast(1)	5	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)															---	---	---	---
CACNA1C	775	broad.mit.edu	37	12	2774091	2774091	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2774091A>G	uc009zdu.1	+	37	4790	c.4477A>G	c.(4477-4479)ACA>GCA	p.T1493A	CACNA1C_uc009zdv.1_Missense_Mutation_p.T1442A|CACNA1C_uc001qkb.2_Missense_Mutation_p.T1445A|CACNA1C_uc001qkc.2_Missense_Mutation_p.T1445A|CACNA1C_uc001qke.2_Missense_Mutation_p.T1434A|CACNA1C_uc001qkf.2_Missense_Mutation_p.T1434A|CACNA1C_uc001qjz.2_Missense_Mutation_p.T1445A|CACNA1C_uc001qkd.2_Missense_Mutation_p.T1445A|CACNA1C_uc001qkg.2_Missense_Mutation_p.T1432A|CACNA1C_uc009zdw.1_Missense_Mutation_p.T1467A|CACNA1C_uc001qkh.2_Missense_Mutation_p.T1434A|CACNA1C_uc001qkl.2_Missense_Mutation_p.T1493A|CACNA1C_uc001qkn.2_Missense_Mutation_p.T1445A|CACNA1C_uc001qko.2_Missense_Mutation_p.T1465A|CACNA1C_uc001qkp.2_Missense_Mutation_p.T1445A|CACNA1C_uc001qkr.2_Missense_Mutation_p.T1462A|CACNA1C_uc001qku.2_Missense_Mutation_p.T1445A|CACNA1C_uc001qkq.2_Missense_Mutation_p.T1473A|CACNA1C_uc001qks.2_Missense_Mutation_p.T1445A|CACNA1C_uc001qkt.2_Missense_Mutation_p.T1445A|CACNA1C_uc001qki.1_Missense_Mutation_p.T1181A|CACNA1C_uc001qkj.1_Missense_Mutation_p.T1181A|CACNA1C_uc001qkk.1_Missense_Mutation_p.T1181A|CACNA1C_uc001qkm.1_Missense_Mutation_p.T1170A|CACNA1C_uc010sea.1_Missense_Mutation_p.T136A	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,	1493	Phenylalkylamine binding (By similarity).|Extracellular (Potential).|Dihydropyridine binding (By similarity).|IV.				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)													---	---	---	---
AKAP3	10566	broad.mit.edu	37	12	4736730	4736730	+	Silent	SNP	C	T	T	rs113770524		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4736730C>T	uc001qnb.3	-	4	1567	c.1338G>A	c.(1336-1338)GCG>GCA	p.A446A		NM_006422	NP_006413	O75969	AKAP3_HUMAN	A-kinase anchor protein 3	446					acrosome reaction|cellular component movement	acrosomal vesicle	protein kinase A binding			skin(3)|large_intestine(1)|ovary(1)|kidney(1)	6																		---	---	---	---
KCNA5	3741	broad.mit.edu	37	12	5154149	5154149	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5154149G>C	uc001qni.2	+	1	1065	c.836G>C	c.(835-837)CGT>CCT	p.R279P		NM_002234	NP_002225	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related	279						Golgi apparatus|voltage-gated potassium channel complex	delayed rectifier potassium channel activity			ovary(2)|breast(2)	4																		---	---	---	---
VWF	7450	broad.mit.edu	37	12	6085337	6085337	+	Silent	SNP	G	A	A	rs142452106	byFrequency;by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6085337G>A	uc001qnn.1	-	43	7627	c.7377C>T	c.(7375-7377)GCC>GCT	p.A2459A	VWF_uc010set.1_Intron	NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein	2459	VWFC 2.				blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)													---	---	---	---
CHD4	1108	broad.mit.edu	37	12	6692525	6692525	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6692525C>A	uc001qpo.2	-	26	4063	c.3899G>T	c.(3898-3900)CGG>CTG	p.R1300L	CHD4_uc001qpn.2_Missense_Mutation_p.R1293L|CHD4_uc001qpp.2_Missense_Mutation_p.R1297L|uc001qpq.1_3'UTR|SCARNA11_uc001qpr.1_5'Flank	NM_001273	NP_001264	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	1300	Poly-Glu.				chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|DNA binding|zinc ion binding			central_nervous_system(2)	2																		---	---	---	---
GPR162	27239	broad.mit.edu	37	12	6933422	6933422	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6933422C>T	uc001qqw.1	+	2	893	c.358C>T	c.(358-360)CGC>TGC	p.R120C	GPR162_uc010sfn.1_Missense_Mutation_p.R120C|GPR162_uc001qqx.1_Intron|GPR162_uc009zfd.1_Intron|GPR162_uc001qqy.1_5'Flank	NM_019858	NP_062832	Q16538	GP162_HUMAN	G protein-coupled receptor 162 isoform 2	120	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
USP5	8078	broad.mit.edu	37	12	6973100	6973100	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6973100C>T	uc001qri.3	+	16	2120	c.2061C>T	c.(2059-2061)GCC>GCT	p.A687A	USP5_uc001qrh.3_Silent_p.A664A	NM_001098536	NP_001092006	P45974	UBP5_HUMAN	ubiquitin specific peptidase 5 isoform 1	687	UBA 1.				positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process	lysosome	cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|zinc ion binding			lung(2)|breast(1)|skin(1)	4																		---	---	---	---
PHB2	11331	broad.mit.edu	37	12	7077092	7077092	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7077092G>A	uc001qsd.2	-	5	780	c.570C>T	c.(568-570)AGC>AGT	p.S190S	PHB2_uc010sft.1_Silent_p.S190S|PHB2_uc010sfu.1_Silent_p.S190S|PHB2_uc001qse.1_5'Flank|PHB2_uc001qsf.1_5'Flank|PHB2_uc009zfn.1_5'Flank|SCARNA12_uc001qsg.2_5'Flank	NM_001144831	NP_001138303	Q99623	PHB2_HUMAN	prohibitin 2 isoform 1	190	Potential.				negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrial inner membrane|nucleus	estrogen receptor binding|receptor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
ACSM4	341392	broad.mit.edu	37	12	7456941	7456941	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7456941T>C	uc001qsx.1	+	1	14	c.14T>C	c.(13-15)TTC>TCC	p.F5S		NM_001080454	NP_001073923	P0C7M7	ACSM4_HUMAN	acyl-CoA synthetase medium-chain family member 4	5					fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|metal ion binding				0																		---	---	---	---
CD163L1	283316	broad.mit.edu	37	12	7551019	7551019	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7551019G>A	uc001qsy.2	-	7	1596	c.1570C>T	c.(1570-1572)CAT>TAT	p.H524Y	CD163L1_uc010sge.1_Missense_Mutation_p.H534Y	NM_174941	NP_777601	Q9NR16	C163B_HUMAN	scavenger receptor cysteine-rich type 1	524	SRCR 5.|Extracellular (Potential).					extracellular region|integral to membrane|plasma membrane	scavenger receptor activity			ovary(8)|skin(2)|central_nervous_system(1)	11																		---	---	---	---
RIMKLB	57494	broad.mit.edu	37	12	8926297	8926297	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8926297C>T	uc001quu.2	+	6	1329	c.1078C>T	c.(1078-1080)CGA>TGA	p.R360*	RIMKLB_uc009zgf.1_Intron|RIMKLB_uc001qux.2_Nonsense_Mutation_p.R360*|RIMKLB_uc010sgl.1_Nonsense_Mutation_p.R360*|RIMKLB_uc001quw.2_Intron	NM_020734	NP_065785	Q9ULI2	RIMKB_HUMAN	ribosomal modification protein rimK-like family	360					protein modification process	cytoplasm	acid-amino acid ligase activity|ATP binding|metal ion binding				0																		---	---	---	---
A2M	2	broad.mit.edu	37	12	9221343	9221343	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9221343G>A	uc001qvk.1	-	34	4472	c.4359C>T	c.(4357-4359)TAC>TAT	p.Y1453Y	A2M_uc001qvj.1_Silent_p.Y495Y|A2M_uc009zgk.1_Silent_p.Y1303Y	NM_000014	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin precursor	1453					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)													---	---	---	---
CSDA	8531	broad.mit.edu	37	12	10856642	10856642	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-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)																	---	---	---	---
TAS2R14	50840	broad.mit.edu	37	12	11090985	11090985	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11090985T>C	uc010shi.1	-	1	822	c.822A>G	c.(820-822)TCA>TCG	p.S274S	PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRB4_uc001qzf.1_Intron|PRH1_uc001qzj.2_RNA	NM_023922	NP_076411	Q9NYV8	T2R14_HUMAN	taste receptor, type 2, member 14	274	Helical; Name=7; (Potential).				detection of chemical stimulus involved in sensory perception of bitter taste		bitter taste receptor activity				0																		---	---	---	---
TAS2R30	259293	broad.mit.edu	37	12	11286153	11286153	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11286153C>T	uc009zhs.1	-	1	691	c.691G>A	c.(691-693)GTG>ATG	p.V231M	PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRB4_uc001qzf.1_Intron|PRH1_uc001qzj.2_Intron	NM_001097643	NP_001091112			type 2 taste receptor member 30												0																		---	---	---	---
ETV6	2120	broad.mit.edu	37	12	12038906	12038906	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12038906A>T	uc001qzz.2	+	7	1473	c.1199A>T	c.(1198-1200)CAC>CTC	p.H400L	ETV6_uc001raa.1_Intron	NM_001987	NP_001978	P41212	ETV6_HUMAN	ets variant 6	400	ETS.					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								---	---	---	---
PTPRO	5800	broad.mit.edu	37	12	15677804	15677804	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15677804A>G	uc001rcv.1	+	11	2122	c.1948A>G	c.(1948-1950)AGT>GGT	p.S650G	PTPRO_uc001rcw.1_Missense_Mutation_p.S650G	NM_030667	NP_109592	Q16827	PTPRO_HUMAN	receptor-type protein tyrosine phosphatase O	650	Fibronectin type-III 7.|Extracellular (Potential).					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)																---	---	---	---
BCAT1	586	broad.mit.edu	37	12	24995049	24995049	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:24995049T>G	uc001rgd.3	-	7	1226	c.784A>C	c.(784-786)AAT>CAT	p.N262H	BCAT1_uc001rgc.2_Missense_Mutation_p.N261H|BCAT1_uc010six.1_Missense_Mutation_p.N274H|BCAT1_uc010siy.1_Missense_Mutation_p.N225H|BCAT1_uc001rge.3_Missense_Mutation_p.N201H	NM_005504	NP_005495	P54687	BCAT1_HUMAN	branched chain aminotransferase 1, cytosolic	262					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)													---	---	---	---
C12orf71	728858	broad.mit.edu	37	12	27235125	27235125	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27235125A>G	uc001rhq.2	-	1	331	c.292T>C	c.(292-294)TCC>CCC	p.S98P		NM_001080406	NP_001073875	A8MTZ7	CL071_HUMAN	hypothetical protein LOC728858	98											0																		---	---	---	---
KLHDC5	57542	broad.mit.edu	37	12	27933753	27933753	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27933753C>A	uc001rij.2	+	1	567	c.490C>A	c.(490-492)CCC>ACC	p.P164T	KLHDC5_uc009zjj.2_RNA	NM_020782	NP_065833	Q9P2K6	KLDC5_HUMAN	kelch domain containing 5	164										ovary(1)|central_nervous_system(1)	2	Lung SC(9;0.0873)																	---	---	---	---
ERGIC2	51290	broad.mit.edu	37	12	29502117	29502117	+	Intron	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29502117G>T	uc001riv.2	-						ERGIC2_uc001riw.2_Intron	NM_016570	NP_057654			PTX1 protein						vesicle-mediated transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi apparatus|integral to membrane|nucleus				ovary(1)	1	Lung NSC(12;2.02e-08)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)|Lung SC(9;0.184)				Arsenic trioxide(DB01169)													---	---	---	---
CAPRIN2	65981	broad.mit.edu	37	12	30869613	30869613	+	Intron	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30869613T>C	uc001rji.1	-						CAPRIN2_uc001rjf.1_Intron|CAPRIN2_uc001rjg.1_Intron|CAPRIN2_uc001rjh.1_Intron|CAPRIN2_uc001rjj.1_Intron|CAPRIN2_uc001rjk.3_Intron|CAPRIN2_uc001rjl.3_Intron|CAPRIN2_uc001rjm.1_Intron	NM_001002259	NP_001002259			C1q domain containing 1 isoform 1						negative regulation of cell growth|negative regulation of translation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of dendrite morphogenesis|positive regulation of dendritic spine morphogenesis|positive regulation of peptidyl-serine phosphorylation|positive regulation of protein binding|positive regulation of transcription from RNA polymerase II promoter	mitochondrion|receptor complex	receptor binding|RNA binding			ovary(1)|central_nervous_system(1)	2	all_lung(12;1.13e-09)|Lung NSC(12;7.98e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)																	---	---	---	---
BICD1	636	broad.mit.edu	37	12	32480437	32480437	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32480437T>G	uc001rku.2	+	5	1129	c.1048T>G	c.(1048-1050)TCA>GCA	p.S350A	BICD1_uc001rkv.2_Missense_Mutation_p.S350A|BICD1_uc010skd.1_RNA	NM_001714	NP_001705	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 isoform 1	350	Potential.				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)															---	---	---	---
LRRK2	120892	broad.mit.edu	37	12	40709040	40709040	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40709040G>A	uc001rmg.3	+	33	4886	c.4765G>A	c.(4765-4767)GCA>ACA	p.A1589T	LRRK2_uc009zjw.2_Missense_Mutation_p.A427T|LRRK2_uc001rmi.2_Missense_Mutation_p.A422T	NM_198578	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1589					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)																---	---	---	---
ADAMTS20	80070	broad.mit.edu	37	12	43821142	43821142	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43821142C>T	uc010skx.1	-	27	4076	c.4076G>A	c.(4075-4077)TGT>TAT	p.C1359Y	ADAMTS20_uc001rno.1_Missense_Mutation_p.C477Y	NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with	1359	TSP type-1 10.					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)														---	---	---	---
IRAK4	51135	broad.mit.edu	37	12	44166771	44166771	+	Nonsense_Mutation	SNP	C	T	T	rs114951157	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44166771C>T	uc001rnu.3	+	6	677	c.547C>T	c.(547-549)CGA>TGA	p.R183*	IRAK4_uc001rnt.3_Nonsense_Mutation_p.R183*|IRAK4_uc001rnx.3_Nonsense_Mutation_p.R59*|IRAK4_uc001rny.3_Nonsense_Mutation_p.R59*|IRAK4_uc010sky.1_Nonsense_Mutation_p.R59*|IRAK4_uc001rnv.3_Nonsense_Mutation_p.R59*|IRAK4_uc001rnw.3_Nonsense_Mutation_p.R59*	NM_001114182	NP_001107654	Q9NWZ3	IRAK4_HUMAN	interleukin-1 receptor-associated kinase 4	183					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|endosome membrane|plasma membrane	ATP binding|magnesium ion binding|protein serine/threonine kinase activity				0	all_cancers(12;0.00149)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.04)														---	---	---	---
RAPGEF3	10411	broad.mit.edu	37	12	48141393	48141393	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48141393A>C	uc009zkp.2	-	14	1804	c.1364T>G	c.(1363-1365)GTG>GGG	p.V455G	RAPGEF3_uc001rpx.2_5'Flank|RAPGEF3_uc010sln.1_Missense_Mutation_p.V19G|RAPGEF3_uc001rpy.2_RNA|RAPGEF3_uc009zkq.2_Missense_Mutation_p.V455G|RAPGEF3_uc001rpz.3_Missense_Mutation_p.V497G|RAPGEF3_uc001rqa.2_Missense_Mutation_p.V19G	NM_001098532	NP_001092002	A8K2G5	A8K2G5_HUMAN	Rap guanine nucleotide exchange factor 3 isoform	455					regulation of protein phosphorylation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cAMP-dependent protein kinase complex	cAMP-dependent protein kinase regulator activity|guanyl-nucleotide exchange factor activity			lung(2)|skin(1)|pancreas(1)	4	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)														---	---	---	---
HDAC7	51564	broad.mit.edu	37	12	48179189	48179189	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48179189C>A	uc010slo.1	-	24	2967	c.2772G>T	c.(2770-2772)GAG>GAT	p.E924D	HDAC7_uc009zku.2_RNA|HDAC7_uc001rqe.2_Missense_Mutation_p.E358D|HDAC7_uc001rqj.3_Missense_Mutation_p.E887D|HDAC7_uc001rqk.3_Missense_Mutation_p.E907D	NM_015401	NP_056216	Q8WUI4	HDAC7_HUMAN	histone deacetylase 7 isoform a	885	Interaction with SIN3A (By similarity).				negative regulation of interleukin-2 production|negative regulation of osteoblast differentiation|positive regulation of cell migration involved in sprouting angiogenesis|transcription, DNA-dependent	cytoplasm|histone deacetylase complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein kinase C binding|repressing transcription factor binding			lung(1)|breast(1)	2				GBM - Glioblastoma multiforme(48;0.137)														---	---	---	---
MLL2	8085	broad.mit.edu	37	12	49424776	49424776	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49424776C>T	uc001rta.3	-	40	13571	c.13571G>A	c.(13570-13572)CGG>CAG	p.R4524Q		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	4524					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	49440398	49440398	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49440398C>T	uc001rta.3	-	15	4412	c.4412G>A	c.(4411-4413)TGC>TAC	p.C1471Y		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	1471	Cys-rich.|PHD-type 4.				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)			---	---	---	---
PRPF40B	25766	broad.mit.edu	37	12	50029029	50029029	+	Silent	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50029029C>A	uc001rur.1	+	12	1147	c.1083C>A	c.(1081-1083)ACC>ACA	p.T361T	PRPF40B_uc001rup.1_Silent_p.T383T|PRPF40B_uc001ruq.1_Silent_p.T355T|PRPF40B_uc001rus.1_Silent_p.T304T	NM_001031698	NP_001026868	Q6NWY9	PR40B_HUMAN	Huntingtin interacting protein C isoform 1	361					mRNA processing|RNA splicing	nuclear speck				skin(2)|ovary(1)|pancreas(1)|kidney(1)	5																		---	---	---	---
LIMA1	51474	broad.mit.edu	37	12	50616263	50616263	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50616263G>A	uc001rwj.3	-	4	345	c.171C>T	c.(169-171)ACC>ACT	p.T57T	LIMA1_uc001rwh.3_5'UTR|LIMA1_uc001rwi.3_5'UTR|LIMA1_uc001rwk.3_Silent_p.T57T|LIMA1_uc010smr.1_RNA|LIMA1_uc010sms.1_RNA	NM_016357	NP_057441	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1 isoform b	57					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																		---	---	---	---
LETMD1	25875	broad.mit.edu	37	12	51453153	51453153	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51453153T>G	uc001rxm.2	+	9	1078	c.1022T>G	c.(1021-1023)CTG>CGG	p.L341R	LETMD1_uc001rxl.2_Missense_Mutation_p.L285R|LETMD1_uc009zlv.2_RNA|LETMD1_uc001rxs.2_Missense_Mutation_p.L146R|LETMD1_uc009zlw.2_Missense_Mutation_p.L354R|LETMD1_uc001rxn.2_Missense_Mutation_p.L184R|LETMD1_uc001rxo.2_RNA|LETMD1_uc001rxp.2_Missense_Mutation_p.L224R|LETMD1_uc001rxq.2_Missense_Mutation_p.L217R|LETMD1_uc001rxr.2_RNA|LETMD1_uc001rxt.2_Missense_Mutation_p.L81R	NM_015416	NP_056231	Q6P1Q0	LTMD1_HUMAN	LETM1 domain containing 1 isoform 1	341	Mitochondrial intermembrane (Potential).|LETM1.					integral to membrane|mitochondrial outer membrane	protein binding			central_nervous_system(2)	2																		---	---	---	---
KRT7	3855	broad.mit.edu	37	12	52628928	52628928	+	Intron	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52628928G>A	uc001saa.1	+						KRT7_uc009zmf.1_Intron	NM_005556	NP_005547			keratin 7						cytoskeleton organization|DNA replication|interphase|interspecies interaction between organisms|regulation of translation	Golgi apparatus|keratin filament|nucleus	protein binding|structural molecule activity				0				BRCA - Breast invasive adenocarcinoma(357;0.105)														---	---	---	---
KRT8	3856	broad.mit.edu	37	12	53293718	53293718	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53293718G>A	uc001sbd.2	-	5	925	c.822C>T	c.(820-822)AGC>AGT	p.S274S	KRT8_uc009zmj.2_Silent_p.S274S|KRT8_uc009zmk.1_Silent_p.S302S|KRT8_uc009zml.1_Silent_p.S274S|KRT8_uc009zmm.1_Silent_p.S274S	NM_002273	NP_002264	P05787	K2C8_HUMAN	keratin 8	274	Necessary for interaction with PNN.|Rod.|Coil 2.				cytoskeleton organization|interspecies interaction between organisms	cytoplasm|keratin filament|nuclear matrix|nucleoplasm	protein binding|structural molecule activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(357;0.108)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
RARG	5916	broad.mit.edu	37	12	53608335	53608335	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53608335A>G	uc001sce.2	-	6	1016	c.531T>C	c.(529-531)CCT>CCC	p.P177P	RARG_uc001scd.2_Silent_p.P166P|RARG_uc010sob.1_Silent_p.P155P|RARG_uc001scf.2_Silent_p.P177P|RARG_uc001scg.2_Silent_p.P105P|RARG_uc010soc.1_Silent_p.P56P|RARG_uc010sod.1_Silent_p.P214P	NM_000966	NP_000957	P13631	RARG_HUMAN	retinoic acid receptor, gamma isoform 1	177	Hinge.				canonical Wnt receptor signaling pathway|embryonic eye morphogenesis|embryonic hindlimb morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter|regulation of cell size|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to retinoic acid	integral to membrane|transcription factor complex	retinoic acid receptor activity|retinoid X receptor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			breast(2)|ovary(1)|lung(1)	4					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tazarotene(DB00799)|Tretinoin(DB00755)													---	---	---	---
ATP5G2	517	broad.mit.edu	37	12	54069856	54069856	+	Intron	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54069856G>T	uc009znc.2	-						ATP5G2_uc001sec.2_Missense_Mutation_p.L41I|ATP5G2_uc001sed.2_Intron	NM_001002031	NP_001002031			ATP synthase, H+ transporting, mitochondrial F0						ATP hydrolysis coupled proton transport|ATP synthesis coupled proton transport	integral to membrane|mitochondrial proton-transporting ATP synthase complex|proton-transporting ATP synthase complex, coupling factor F(o)	hydrogen ion transmembrane transporter activity|lipid binding			ovary(1)	1																OREG0021876	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
NFE2	4778	broad.mit.edu	37	12	54686313	54686313	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54686313G>A	uc009znk.2	-	2	1477	c.967C>T	c.(967-969)CGC>TGC	p.R323C	NFE2_uc001sfq.2_Missense_Mutation_p.R323C|NFE2_uc001sfr.3_Missense_Mutation_p.R323C|NFE2_uc009znl.2_Missense_Mutation_p.R323C	NM_006163	NP_006154	Q16621	NFE2_HUMAN	nuclear factor, erythroid derived 2 isoform 1	323	Leucine-zipper.				blood circulation|blood coagulation|multicellular organismal development|nucleosome disassembly|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter	actin cytoskeleton|cytoplasm|PML body	protein dimerization activity|protein N-terminus binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|WW domain binding				0																		---	---	---	---
OR6C6	283365	broad.mit.edu	37	12	55688405	55688405	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55688405T>C	uc010sph.1	-	1	612	c.612A>G	c.(610-612)ACA>ACG	p.T204T		NM_001005493	NP_001005493	A6NF89	OR6C6_HUMAN	olfactory receptor, family 6, subfamily C,	204	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)|skin(1)	2																		---	---	---	---
OR6C6	283365	broad.mit.edu	37	12	55688771	55688771	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55688771G>A	uc010sph.1	-	1	246	c.246C>T	c.(244-246)ACC>ACT	p.T82T		NM_001005493	NP_001005493	A6NF89	OR6C6_HUMAN	olfactory receptor, family 6, subfamily C,	82	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)|skin(1)	2																		---	---	---	---
DNAJC14	85406	broad.mit.edu	37	12	56221359	56221359	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56221359C>T	uc001shx.1	-	2	1288	c.1084G>A	c.(1084-1086)GCT>ACT	p.A362T	DNAJC14_uc001shu.1_Missense_Mutation_p.A362T|DNAJC14_uc009zob.1_Missense_Mutation_p.A362T|DNAJC14_uc001shy.1_Missense_Mutation_p.A362T	NM_032364	NP_115740	Q6Y2X3	DJC14_HUMAN	dopamine receptor interacting protein	362					protein folding|protein transport	endoplasmic reticulum membrane|integral to membrane	heat shock protein binding|unfolded protein binding			ovary(3)|large_intestine(1)	4																		---	---	---	---
CS	1431	broad.mit.edu	37	12	56667591	56667591	+	Intron	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56667591T>C	uc001sks.1	-						CS_uc010sql.1_Intron|CS_uc001skr.1_Intron|CS_uc001skt.1_Intron|CS_uc010sqm.1_Intron	NM_004077	NP_004068			citrate synthase precursor						cellular carbohydrate metabolic process|tricarboxylic acid cycle	mitochondrial matrix	citrate (Si)-synthase activity				0		Myeloproliferative disorder(1001;0.000374)		BRCA - Breast invasive adenocarcinoma(357;6.17e-07)														---	---	---	---
ZBTB39	9880	broad.mit.edu	37	12	57397832	57397832	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57397832C>T	uc001sml.1	-	2	956	c.870G>A	c.(868-870)CAG>CAA	p.Q290Q	RDH16_uc010sqx.1_5'Flank	NM_014830	NP_055645	O15060	ZBT39_HUMAN	zinc finger and BTB domain containing 39	290					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1																		---	---	---	---
LRP1	4035	broad.mit.edu	37	12	57561246	57561246	+	Silent	SNP	C	T	T	rs149857225	byFrequency;by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57561246C>T	uc001snd.2	+	19	3400	c.2934C>T	c.(2932-2934)CCC>CCT	p.P978P	LRP1_uc009zph.1_RNA|LRP1_uc009zpi.1_5'Flank	NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	978	Extracellular (Potential).|LDL-receptor class A 6.				aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity			ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2)	22				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)													---	---	---	---
LRP1	4035	broad.mit.edu	37	12	57605344	57605344	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57605344T>C	uc001snd.2	+	85	13632	c.13166T>C	c.(13165-13167)ATG>ACG	p.M4389T		NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	4389	Extracellular (Potential).|EGF-like 22.				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)													---	---	---	---
AVIL	10677	broad.mit.edu	37	12	58201388	58201388	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58201388G>A	uc001sqj.1	-	11	1346	c.1317C>T	c.(1315-1317)ATC>ATT	p.I439I	AVIL_uc009zqe.1_Silent_p.I432I|AVIL_uc001sqk.1_5'UTR|AVIL_uc001sql.3_Silent_p.I416I	NM_006576	NP_006567	O75366	AVIL_HUMAN	advillin	439	Gelsolin-like 4.|Core (By similarity).				actin filament capping|cilium morphogenesis|cytoskeleton organization|positive regulation of neuron projection development	actin cytoskeleton|axon|cytoplasm	actin binding			central_nervous_system(1)	1	Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)																	---	---	---	---
C12orf66	144577	broad.mit.edu	37	12	64587679	64587679	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64587679T>C	uc001srw.3	-	3	1340	c.1281A>G	c.(1279-1281)TCA>TCG	p.S427S	C12orf66_uc009zql.2_Silent_p.S374S	NM_152440	NP_689653	Q96MD2	CL066_HUMAN	hypothetical protein LOC144577	427										ovary(1)	1																		---	---	---	---
KCNMB4	27345	broad.mit.edu	37	12	70760802	70760802	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70760802T>C	uc001svx.2	+	1	741	c.288T>C	c.(286-288)TCT>TCC	p.S96S		NM_014505	NP_055320	Q86W47	KCMB4_HUMAN	calcium-activated potassium channel beta 4	96	Extracellular (Potential).				detection of calcium ion|platelet activation|regulation of action potential in neuron|regulation of neurotransmitter secretion|regulation of vasoconstriction|synaptic transmission	voltage-gated potassium channel complex	calcium-activated potassium channel activity|protein binding				0	Renal(347;0.236)		Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)															---	---	---	---
TRHDE	29953	broad.mit.edu	37	12	72962430	72962430	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72962430A>G	uc001sxa.2	+	10	2020	c.1990A>G	c.(1990-1992)AAA>GAA	p.K664E		NM_013381	NP_037513	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	664	Extracellular (Potential).				cell-cell signaling|proteolysis|signal transduction	integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
KITLG	4254	broad.mit.edu	37	12	88909307	88909307	+	Intron	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88909307T>G	uc001tav.2	-						KITLG_uc009zsn.2_Intron|KITLG_uc001taw.2_Intron|KITLG_uc009zso.1_Intron	NM_000899	NP_000890			KIT ligand isoform b precursor						cell adhesion|cell proliferation|hemopoiesis|male gonad development|positive regulation of DNA replication|signal transduction	cytoplasm|cytoskeleton|integral to membrane|plasma membrane	growth factor activity|identical protein binding|stem cell factor receptor binding			ovary(1)	1														Testicular_Cancer_Familial_Clustering_of				---	---	---	---
CCDC41	51134	broad.mit.edu	37	12	94805529	94805529	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94805529C>A	uc001tdd.2	-	4	854	c.268G>T	c.(268-270)GAA>TAA	p.E90*	CCDC41_uc001tde.2_Nonsense_Mutation_p.E90*|CCDC41_uc009zsw.1_RNA|CCDC41_uc001tdf.2_Nonsense_Mutation_p.E90*	NM_016122	NP_057206	Q9Y592	CCD41_HUMAN	NY-REN-58 antigen	82	Potential.										0																		---	---	---	---
HAL	3034	broad.mit.edu	37	12	96384199	96384199	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96384199G>T	uc001tem.1	-	10	1124	c.827C>A	c.(826-828)CCG>CAG	p.P276Q	HAL_uc009zti.1_RNA|HAL_uc010suw.1_Missense_Mutation_p.P68Q|HAL_uc010sux.1_Missense_Mutation_p.P276Q	NM_002108	NP_002099	P42357	HUTH_HUMAN	histidine ammonia-lyase	276					biosynthetic process|histidine catabolic process	cytosol	histidine ammonia-lyase activity			ovary(2)|skin(1)	3					L-Histidine(DB00117)													---	---	---	---
FAM71C	196472	broad.mit.edu	37	12	100042262	100042262	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100042262A>G	uc001tgn.2	+	1	732	c.310A>G	c.(310-312)ACC>GCC	p.T104A	ANKS1B_uc001tge.1_Intron|ANKS1B_uc001tgf.1_Intron|ANKS1B_uc009ztt.1_Intron	NM_153364	NP_699195	Q8NEG0	FA71C_HUMAN	hypothetical protein LOC196472	104											0				OV - Ovarian serous cystadenocarcinoma(2;0.00733)|Epithelial(2;0.0385)|all cancers(2;0.19)														---	---	---	---
GNPTAB	79158	broad.mit.edu	37	12	102179826	102179826	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102179826T>C	uc001tit.2	-	5	714	c.535A>G	c.(535-537)AAT>GAT	p.N179D	GNPTAB_uc001tiu.1_Missense_Mutation_p.N179D|GNPTAB_uc001tiv.3_Missense_Mutation_p.N42D	NM_024312	NP_077288	Q3T906	GNPTA_HUMAN	N-acetylglucosamine-1-phosphate transferase	179					cell differentiation	Golgi membrane|integral to membrane|nucleus	metal ion binding|transcription factor binding|UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity			ovary(1)|skin(1)	2																		---	---	---	---
STAB2	55576	broad.mit.edu	37	12	104089528	104089528	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104089528C>T	uc001tjw.2	+	33	3674	c.3488C>T	c.(3487-3489)GCG>GTG	p.A1163V		NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor	1163	Extracellular (Potential).|FAS1 4.				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																		---	---	---	---
PWP1	11137	broad.mit.edu	37	12	108102967	108102967	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108102967A>G	uc001tmo.1	+	13	1335	c.1248A>G	c.(1246-1248)TTA>TTG	p.L416L	PWP1_uc009zuu.1_Silent_p.L416L	NM_007062	NP_008993	Q13610	PWP1_HUMAN	periodic tryptophan protein 1	416	WD 4.				transcription, DNA-dependent	nucleus					0																		---	---	---	---
BRAP	8315	broad.mit.edu	37	12	112120948	112120948	+	Splice_Site	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112120948A>G	uc001tsn.3	-	2	438	c.244_splice	c.e2+1	p.D82_splice	BRAP_uc010syh.1_5'Flank|BRAP_uc009zvv.2_Splice_Site_p.D52_splice|ACAD10_uc009zvw.2_5'Flank|ACAD10_uc001tso.3_5'Flank|ACAD10_uc001tsp.2_5'Flank|ACAD10_uc009zvx.2_5'Flank|ACAD10_uc001tsq.2_5'Flank	NM_006768	NP_006759			BRCA1 associated protein						MAPKKK cascade|negative regulation of signal transduction|Ras protein signal transduction	cytoplasm|ubiquitin ligase complex	identical protein binding|nuclear localization sequence binding|nucleotide binding|ubiquitin-protein ligase activity|zinc ion binding			lung(1)	1																		---	---	---	---
MAPKAPK5	8550	broad.mit.edu	37	12	112305438	112305438	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112305438T>C	uc001tta.2	+	4	508	c.249T>C	c.(247-249)GCT>GCC	p.A83A	MAPKAPK5_uc001tsz.2_Silent_p.A83A|MAPKAPK5_uc001ttb.2_Silent_p.A16A	NM_139078	NP_620777	Q8IW41	MAPK5_HUMAN	MAP kinase-activated protein kinase 5 isoform 2	83	Protein kinase.				signal transduction	cytoplasm|nucleus	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity			lung(2)|ovary(1)	3																		---	---	---	---
C12orf51	283450	broad.mit.edu	37	12	112616880	112616880	+	Silent	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112616880T>G	uc009zwc.2	-	57	9970	c.9952A>C	c.(9952-9954)AGG>CGG	p.R3318R		NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2																		---	---	---	---
OAS3	4940	broad.mit.edu	37	12	113387000	113387000	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113387000G>A	uc001tug.2	+	6	1451	c.1364G>A	c.(1363-1365)AGA>AAA	p.R455K		NM_006187	NP_006178	Q9Y6K5	OAS3_HUMAN	2'-5'oligoadenylate synthetase 3	455	OAS domain 2.				interferon-gamma-mediated signaling pathway|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|type I interferon-mediated signaling pathway	microsome	ATP binding|nucleotidyltransferase activity|RNA binding			central_nervous_system(1)	1																		---	---	---	---
TBX5	6910	broad.mit.edu	37	12	114793719	114793719	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114793719C>T	uc001tvo.2	-	9	1670	c.1175G>A	c.(1174-1176)AGC>AAC	p.S392N	TBX5_uc001tvp.2_Missense_Mutation_p.S392N|TBX5_uc001tvq.2_Missense_Mutation_p.S342N	NM_181486	NP_852259	Q99593	TBX5_HUMAN	T-box 5 isoform 1	392					cardiac left ventricle formation|cell migration involved in coronary vasculogenesis|cell-cell signaling|embryonic arm morphogenesis|induction of apoptosis|negative regulation of cardiac muscle cell proliferation|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|pericardium development|positive regulation of cardioblast differentiation|positive regulation of transcription from RNA polymerase II promoter|ventricular septum development	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			ovary(6)|pancreas(1)|skin(1)	8	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0893)														---	---	---	---
HSPB8	26353	broad.mit.edu	37	12	119631565	119631565	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119631565A>G	uc001txb.2	+	3	1016	c.493A>G	c.(493-495)ATC>GTC	p.I165V	HSPB8_uc001txc.2_3'UTR	NM_014365	NP_055180	Q9UJY1	HSPB8_HUMAN	heat shock 22kDa protein 8	165					cell death|response to heat	cytoplasm|nucleus	identical protein binding|protein serine/threonine kinase activity			central_nervous_system(1)|skin(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
RNF34	80196	broad.mit.edu	37	12	121858086	121858086	+	Silent	SNP	T	C	C	rs77544919		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121858086T>C	uc001ual.1	+	4	789	c.675T>C	c.(673-675)GAT>GAC	p.D225D	RNF34_uc001uak.1_Silent_p.D226D|RNF34_uc001uam.1_Silent_p.D225D	NM_025126	NP_079402	Q969K3	RNF34_HUMAN	ring finger protein 34 isoform 2	225	Asp-rich.				apoptosis	endomembrane system|membrane|nuclear speck	ligase activity|zinc ion binding				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000432)|Epithelial(86;0.00233)														---	---	---	---
ORAI1	84876	broad.mit.edu	37	12	122079166	122079166	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122079166G>A	uc010szz.1	+	3	716	c.523G>A	c.(523-525)GCC>ACC	p.A175T		NM_032790	NP_116179	Q96D31	CRCM1_HUMAN	calcium release-activated calcium channel	175	Helical; (Potential).				platelet activation|positive regulation of calcium ion transport	integral to plasma membrane	protein binding|store-operated calcium channel activity				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000415)|Epithelial(86;0.00148)														---	---	---	---
CLIP1	6249	broad.mit.edu	37	12	122845598	122845598	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122845598C>T	uc001ucg.1	-	4	1019	c.913G>A	c.(913-915)GCC>ACC	p.A305T	CLIP1_uc001uch.1_Missense_Mutation_p.A305T|CLIP1_uc001uci.1_Missense_Mutation_p.A305T|CLIP1_uc001ucj.1_Missense_Mutation_p.A6T|CLIP1_uc010tae.1_Missense_Mutation_p.A305T	NM_002956	NP_002947	P30622	CLIP1_HUMAN	restin isoform a	305	Ser-rich.				mitotic prometaphase|positive regulation of microtubule polymerization	centrosome|cytosol|endosome|intermediate filament|kinetochore	nucleic acid binding|protein homodimerization activity|zinc ion binding			ovary(2)|breast(1)	3	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)														---	---	---	---
KNTC1	9735	broad.mit.edu	37	12	123075917	123075917	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123075917C>T	uc001ucv.2	+	42	4325	c.4162C>T	c.(4162-4164)CTC>TTC	p.L1388F	KNTC1_uc010taf.1_Intron	NM_014708	NP_055523	P50748	KNTC1_HUMAN	Rough Deal homolog, centromere/kinetochore	1388					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)														---	---	---	---
DDX55	57696	broad.mit.edu	37	12	124099807	124099807	+	Silent	SNP	C	T	T	rs11612770	byFrequency;by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124099807C>T	uc001ufi.2	+	9	924	c.900C>T	c.(898-900)CAC>CAT	p.H300H	DDX55_uc001ufh.2_Silent_p.H153H|DDX55_uc001ufj.1_Silent_p.H153H|DDX55_uc001ufk.2_Silent_p.H153H	NM_020936	NP_065987	Q8NHQ9	DDX55_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 55	300	Helicase C-terminal.						ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000142)|Epithelial(86;0.000637)|all cancers(50;0.00772)														---	---	---	---
DNAH10	196385	broad.mit.edu	37	12	124268735	124268735	+	Intron	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124268735T>C	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)														---	---	---	---
TMEM132D	121256	broad.mit.edu	37	12	129559446	129559446	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129559446C>T	uc009zyl.1	-	9	2602	c.2274G>A	c.(2272-2274)GCG>GCA	p.A758A	TMEM132D_uc001uia.2_Silent_p.A296A	NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor	758	Extracellular (Potential).					integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)														---	---	---	---
TMEM132D	121256	broad.mit.edu	37	12	129566495	129566495	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129566495G>A	uc009zyl.1	-	7	2060	c.1732C>T	c.(1732-1734)CGG>TGG	p.R578W	TMEM132D_uc001uia.2_Missense_Mutation_p.R116W	NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor	578	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)														---	---	---	---
FZD10	11211	broad.mit.edu	37	12	130648357	130648357	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130648357C>T	uc001uii.2	+	1	1326	c.870C>T	c.(868-870)TGC>TGT	p.C290C	uc001uig.1_5'Flank|uc001uih.1_5'Flank	NM_007197	NP_009128	Q9ULW2	FZD10_HUMAN	frizzled 10 precursor	290	Extracellular (Potential).				brain development|canonical Wnt receptor signaling pathway|cellular response to retinoic acid|embryo development|gonad development|negative regulation of Rho GTPase activity|neuron differentiation|non-canonical Wnt receptor signaling pathway|positive regulation of JUN kinase activity|positive regulation of Rac GTPase activity|regulation of actin cytoskeleton organization|vasculature development	cell projection|cell surface|cytoplasm|integral to plasma membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			lung(3)|breast(1)|central_nervous_system(1)	5	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.3e-06)|Epithelial(86;1.66e-05)|all cancers(50;5.18e-05)														---	---	---	---
DDX51	317781	broad.mit.edu	37	12	132625395	132625395	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132625395G>A	uc001ujy.3	-	9	1460	c.1421C>T	c.(1420-1422)GCC>GTC	p.A474V		NM_175066	NP_778236	Q8N8A6	DDX51_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 51	474					rRNA processing	nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			lung(1)|pancreas(1)	2	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.59e-08)|Epithelial(86;3.62e-07)|all cancers(50;2.13e-05)														---	---	---	---
POLE	5426	broad.mit.edu	37	12	133202312	133202312	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133202312C>T	uc001uks.1	-	47	6620	c.6576G>A	c.(6574-6576)GCG>GCA	p.A2192A	POLE_uc001ukq.1_Silent_p.A402A|POLE_uc001ukr.1_Silent_p.A996A|POLE_uc010tbq.1_RNA	NM_006231	NP_006222	Q07864	DPOE1_HUMAN	DNA-directed DNA polymerase epsilon	2192					base-excision repair, gap-filling|DNA synthesis involved in DNA repair|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	chromatin binding|DNA binding|DNA-directed DNA polymerase activity|nucleotide binding|protein binding|zinc ion binding			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)									DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
XPO4	64328	broad.mit.edu	37	13	21417997	21417997	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21417997G>A	uc001unq.3	-	5	521	c.485C>T	c.(484-486)GCG>GTG	p.A162V	XPO4_uc010tcr.1_Missense_Mutation_p.A88V	NM_022459	NP_071904	Q9C0E2	XPO4_HUMAN	exportin 4	162					protein transport	cytoplasm|nucleus	protein binding			large_intestine(1)|ovary(1)|kidney(1)	3		all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548)														---	---	---	---
SACS	26278	broad.mit.edu	37	13	23911375	23911375	+	Missense_Mutation	SNP	G	T	T	rs138379074		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23911375G>T	uc001uon.2	-	10	7229	c.6640C>A	c.(6640-6642)CGC>AGC	p.R2214S	SACS_uc001uoo.2_Missense_Mutation_p.R2067S|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron	NM_014363	NP_055178	Q9NZJ4	SACS_HUMAN	sacsin	2214					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)														---	---	---	---
TNFRSF19	55504	broad.mit.edu	37	13	24234625	24234625	+	Silent	SNP	C	A	A	rs147110068		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24234625C>A	uc001uov.1	+	7	796	c.732C>A	c.(730-732)ACC>ACA	p.T244T	TNFRSF19_uc001uot.2_Silent_p.T244T|TNFRSF19_uc010tcu.1_Silent_p.T112T|TNFRSF19_uc001uow.2_Silent_p.T244T	NM_018647	NP_061117	Q9NS68	TNR19_HUMAN	tumor necrosis factor receptor superfamily,	244	Cytoplasmic (Potential).				apoptosis|induction of apoptosis|JNK cascade	integral to membrane|mitochondrion	tumor necrosis factor receptor activity			kidney(1)|skin(1)	2		all_cancers(29;3.4e-22)|all_epithelial(30;8.75e-19)|all_lung(29;5.09e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00193)|Epithelial(112;0.0137)|OV - Ovarian serous cystadenocarcinoma(117;0.0465)|GBM - Glioblastoma multiforme(144;0.184)|Lung(94;0.19)														---	---	---	---
RNF17	56163	broad.mit.edu	37	13	25376662	25376662	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25376662T>C	uc001upr.2	+	14	1943	c.1902T>C	c.(1900-1902)GAT>GAC	p.D634D	RNF17_uc010tdd.1_Silent_p.D493D|RNF17_uc010aab.2_RNA|RNF17_uc010tde.1_Silent_p.D634D|RNF17_uc001ups.2_Silent_p.D573D	NM_031277	NP_112567	Q9BXT8	RNF17_HUMAN	ring finger protein 17	634					multicellular organismal development	cytoplasm|nucleus	hydrolase activity, acting on ester bonds|nucleic acid binding|zinc ion binding			ovary(1)|skin(1)	2		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)														---	---	---	---
PAN3	255967	broad.mit.edu	37	13	28841007	28841007	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28841007A>G	uc001urz.2	+	9	1137	c.1129A>G	c.(1129-1131)ATA>GTA	p.I377V	PAN3_uc010tdo.1_Missense_Mutation_p.I523V|PAN3_uc001ury.2_Missense_Mutation_p.I211V|PAN3_uc001urx.2_Missense_Mutation_p.I323V	NM_175854	NP_787050	Q58A45	PAN3_HUMAN	PABP1-dependent poly A-specific ribonuclease	523	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)														---	---	---	---
HSPH1	10808	broad.mit.edu	37	13	31717998	31717998	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31717998T>C	uc001utj.2	-	12	2045	c.1647A>G	c.(1645-1647)CAA>CAG	p.Q549Q	HSPH1_uc001utk.2_Intron|HSPH1_uc010aaw.2_Silent_p.Q508Q|HSPH1_uc001utl.2_Silent_p.Q551Q|HSPH1_uc010tds.1_Silent_p.Q473Q	NM_006644	NP_006635	Q92598	HS105_HUMAN	heat shock 105kD	549					positive regulation of MHC class I biosynthetic process|positive regulation of NK T cell activation|response to unfolded protein	cytoplasm|extracellular region	ATP binding				0		Lung SC(185;0.0257)		all cancers(112;0.00385)|Epithelial(112;0.0328)|OV - Ovarian serous cystadenocarcinoma(117;0.0375)|GBM - Glioblastoma multiforme(144;0.125)														---	---	---	---
B3GALTL	145173	broad.mit.edu	37	13	31891767	31891767	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31891767C>T	uc010aaz.2	+	13	1239	c.1129C>T	c.(1129-1131)CGC>TGC	p.R377C	B3GALTL_uc001utn.3_RNA	NM_194318	NP_919299	Q6Y288	B3GLT_HUMAN	beta 1,3-galactosyltransferase-like	377	Lumenal (Potential).				fucose metabolic process	endoplasmic reticulum membrane|integral to membrane	transferase activity, transferring glycosyl groups			ovary(2)	2		Lung SC(185;0.0257)		all cancers(112;0.00436)|Epithelial(112;0.0285)|OV - Ovarian serous cystadenocarcinoma(117;0.0512)|GBM - Glioblastoma multiforme(144;0.184)														---	---	---	---
FRY	10129	broad.mit.edu	37	13	32823712	32823712	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32823712G>A	uc001utx.2	+	49	7554	c.7058G>A	c.(7057-7059)CGT>CAT	p.R2353H	FRY_uc010tdw.1_RNA	NM_023037	NP_075463	Q5TBA9	FRY_HUMAN	furry homolog	2353					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	33344508	33344508	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33344508C>T	uc010abf.2	+	32	4032	c.3874C>T	c.(3874-3876)CGA>TGA	p.R1292*	PDS5B_uc010abg.2_RNA	NM_015032	NP_055847	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog	1292	A.T hook 2.				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)														---	---	---	---
MIR320D-1	100302230	broad.mit.edu	37	13	41302008	41302008	+	RNA	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41302008A>C	hsa-mir-320d-1|MI0008190	-			c.4A>C																				0																		---	---	---	---
WBP4	11193	broad.mit.edu	37	13	41642877	41642877	+	Intron	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41642877A>C	uc001uxt.2	+						WBP4_uc010tfd.1_Intron	NM_007187	NP_009118			WW domain-containing binding protein 4						nuclear mRNA cis splicing, via spliceosome	nuclear speck|spliceosomal complex	nucleic acid binding|proline-rich region binding|zinc ion binding			breast(2)|kidney(1)	3		Lung NSC(96;3.55e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;3.11e-09)|Epithelial(112;3.37e-06)|OV - Ovarian serous cystadenocarcinoma(117;8.3e-05)|GBM - Glioblastoma multiforme(144;0.00102)|BRCA - Breast invasive adenocarcinoma(63;0.07)														---	---	---	---
KBTBD7	84078	broad.mit.edu	37	13	41767950	41767950	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41767950G>A	uc001uxw.1	-	1	753	c.444C>T	c.(442-444)TCC>TCT	p.S148S	uc001uxv.1_Intron	NM_032138	NP_115514	Q8WVZ9	KBTB7_HUMAN	kelch repeat and BTB (POZ) domain containing 7	148							protein binding			ovary(1)	1		Lung NSC(96;0.000105)|Breast(139;0.00715)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.21e-09)|Epithelial(112;6.99e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000196)|GBM - Glioblastoma multiforme(144;0.000857)|BRCA - Breast invasive adenocarcinoma(63;0.0669)														---	---	---	---
KBTBD7	84078	broad.mit.edu	37	13	41768039	41768039	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41768039C>T	uc001uxw.1	-	1	664	c.355G>A	c.(355-357)GCC>ACC	p.A119T	uc001uxv.1_Intron	NM_032138	NP_115514	Q8WVZ9	KBTB7_HUMAN	kelch repeat and BTB (POZ) domain containing 7	119	BTB.						protein binding			ovary(1)	1		Lung NSC(96;0.000105)|Breast(139;0.00715)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.21e-09)|Epithelial(112;6.99e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000196)|GBM - Glioblastoma multiforme(144;0.000857)|BRCA - Breast invasive adenocarcinoma(63;0.0669)														---	---	---	---
TSC22D1	8848	broad.mit.edu	37	13	45147375	45147375	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45147375G>T	uc001uzn.3	-	1	3327	c.2836C>A	c.(2836-2838)CTA>ATA	p.L946I	TSC22D1_uc001uzo.1_Intron	NM_183422	NP_904358	Q15714	T22D1_HUMAN	TSC22 domain family, member 1 isoform 1	946					transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding transcription factor activity				0		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)														---	---	---	---
ZC3H13	23091	broad.mit.edu	37	13	46537984	46537984	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46537984T>G	uc010tfw.1	-	16	4671	c.4665A>C	c.(4663-4665)AAA>AAC	p.K1555N	ZC3H13_uc001vaq.2_Missense_Mutation_p.K140N|ZC3H13_uc001vas.1_Missense_Mutation_p.K1556N	NM_015070	NP_055885	Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	1555							nucleic acid binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(96;7.26e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;4.18e-05)														---	---	---	---
ZC3H13	23091	broad.mit.edu	37	13	46549832	46549832	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46549832C>T	uc010tfw.1	-	11	2060	c.2054G>A	c.(2053-2055)CGA>CAA	p.R685Q	ZC3H13_uc001vas.1_Missense_Mutation_p.R685Q|ZC3H13_uc001vat.1_Missense_Mutation_p.R685Q	NM_015070	NP_055885	Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	685	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)														---	---	---	---
ATP7B	540	broad.mit.edu	37	13	52548700	52548700	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52548700A>G	uc001vfw.2	-	2	813	c.656T>C	c.(655-657)CTG>CCG	p.L219P	ATP7B_uc010adv.2_Missense_Mutation_p.L219P|ATP7B_uc001vfx.2_Missense_Mutation_p.L219P|ATP7B_uc001vfy.2_Missense_Mutation_p.L219P|ATP7B_uc010tgt.1_Missense_Mutation_p.L219P|ATP7B_uc010tgu.1_Missense_Mutation_p.L219P|ATP7B_uc010tgv.1_Missense_Mutation_p.L219P|ATP7B_uc010tgw.1_Missense_Mutation_p.L187P	NM_000053	NP_000044	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	219	Cytoplasmic (Potential).				ATP biosynthetic process|cellular copper ion homeostasis|copper ion import|response to copper ion|sequestering of calcium ion	Golgi membrane|integral to plasma membrane|late endosome|mitochondrion	ATP binding|copper ion binding|copper-exporting ATPase activity|protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)										Wilson_disease				---	---	---	---
PCDH17	27253	broad.mit.edu	37	13	58206951	58206951	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58206951G>A	uc001vhq.1	+	1	1163	c.271G>A	c.(271-273)GAC>AAC	p.D91N	PCDH17_uc010aec.1_Missense_Mutation_p.D91N	NM_001040429	NP_001035519	O14917	PCD17_HUMAN	protocadherin 17 precursor	91	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding			ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	7		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)														---	---	---	---
DIAPH3	81624	broad.mit.edu	37	13	60566672	60566672	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60566672C>T	uc001vht.2	-	10	1279	c.1060G>A	c.(1060-1062)GAT>AAT	p.D354N	DIAPH3_uc001vhu.2_Missense_Mutation_p.D91N|DIAPH3_uc001vhv.2_5'Flank|DIAPH3_uc001vhw.1_Missense_Mutation_p.D343N|DIAPH3_uc010aed.1_Missense_Mutation_p.D308N|DIAPH3_uc010aee.1_Missense_Mutation_p.D284N	NM_001042517	NP_001035982	Q9NSV4	DIAP3_HUMAN	diaphanous homolog 3 isoform a	354	GBD/FH3.				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)														---	---	---	---
SLAIN1	122060	broad.mit.edu	37	13	78335006	78335006	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78335006G>A	uc010thy.1	+	6	1009	c.966G>A	c.(964-966)GGG>GGA	p.G322G	SLAIN1_uc001vkk.1_Silent_p.G245G|SLAIN1_uc001vkl.1_Silent_p.G201G|SLAIN1_uc010thz.1_Silent_p.G200G|SLAIN1_uc010aex.1_Silent_p.G87G|SLAIN1_uc010aey.1_Silent_p.G87G|SLAIN1_uc001vkm.2_Silent_p.G201G	NM_144595	NP_653196	Q8ND83	SLAI1_HUMAN	SLAIN motif family, member 1 B	464										ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0853)														---	---	---	---
SPRY2	10253	broad.mit.edu	37	13	80911023	80911023	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80911023T>A	uc001vli.2	-	2	1796	c.818A>T	c.(817-819)AAG>ATG	p.K273M	SPRY2_uc001vlj.2_Missense_Mutation_p.K273M	NM_005842	NP_005833	O43597	SPY2_HUMAN	sprouty 2	273	SPR.|Cys-rich.				epidermal growth factor receptor signaling pathway|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|positive regulation of ERK1 and ERK2 cascade|positive regulation of gene expression|positive regulation of peptidyl-serine phosphorylation|positive regulation of protein kinase B signaling cascade	cytosol|microtubule|ruffle membrane	protein serine/threonine kinase activator activity			ovary(1)|lung(1)	2	Medulloblastoma(90;0.18)	Acute lymphoblastic leukemia(28;0.218)|Breast(118;0.244)		GBM - Glioblastoma multiforme(99;0.0318)														---	---	---	---
DZIP1	22873	broad.mit.edu	37	13	96239947	96239947	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96239947G>C	uc001vmk.2	-	20	2916	c.2064C>G	c.(2062-2064)GAC>GAG	p.D688E	DZIP1_uc001vmi.2_5'UTR|DZIP1_uc001vmj.2_Missense_Mutation_p.D164E|DZIP1_uc001vml.2_Missense_Mutation_p.D669E	NM_198968	NP_945319	Q86YF9	DZIP1_HUMAN	DAZ interacting protein 1 isoform 2	688					germ cell development|multicellular organismal development|spermatogenesis	cytoplasm|nucleus	nucleic acid binding|protein binding|zinc ion binding			ovary(2)	2	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)															---	---	---	---
RNF113B	140432	broad.mit.edu	37	13	98829094	98829094	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98829094G>A	uc001vnk.2	-	1	428	c.397C>T	c.(397-399)CGG>TGG	p.R133W	FARP1_uc001vnh.2_Intron|FARP1_uc001vni.2_Intron|FARP1_uc001vnj.2_Intron	NM_178861	NP_849192	Q8IZP6	R113B_HUMAN	ring finger protein 113B	133							nucleic acid binding|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.13)															---	---	---	---
TMTC4	84899	broad.mit.edu	37	13	101287341	101287341	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101287341G>A	uc001vou.2	-	10	1414	c.1254C>T	c.(1252-1254)AGC>AGT	p.S418S	TMTC4_uc001vot.2_Silent_p.S437S|TMTC4_uc010tja.1_Silent_p.S307S|TMTC4_uc001vov.1_Silent_p.S163S|TMTC4_uc001vow.1_Silent_p.S201S	NM_001079669	NP_001073137	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat	418	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)																	---	---	---	---
KDELC1	79070	broad.mit.edu	37	13	103443336	103443336	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103443336G>A	uc001vpq.3	-	6	1382	c.998C>T	c.(997-999)GCT>GTT	p.A333V	KDELC1_uc001vpr.3_Missense_Mutation_p.A114V	NM_024089	NP_076994	Q6UW63	KDEL1_HUMAN	KDEL (Lys-Asp-Glu-Leu) containing 1 precursor	333						endoplasmic reticulum lumen				ovary(1)	1	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)																	---	---	---	---
ERCC5	2073	broad.mit.edu	37	13	103524624	103524624	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103524624C>T	uc001vpw.2	+	13	3198	c.2755C>T	c.(2755-2757)CGG>TGG	p.R919W	ERCC5_uc001vpu.1_Missense_Mutation_p.R1373W|ERCC5_uc010tjc.1_RNA|ERCC5_uc010tjd.1_Missense_Mutation_p.R751W	NM_000123	NP_000114	P28715	ERCC5_HUMAN	XPG-complementing protein	919					negative regulation of apoptosis|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|response to UV-C|transcription-coupled nucleotide-excision repair|UV protection	nucleoplasm	bubble DNA binding|double-stranded DNA binding|endodeoxyribonuclease activity|metal ion binding|protein homodimerization activity|protein N-terminus binding|single-stranded DNA binding			ovary(4)|lung(1)|central_nervous_system(1)|skin(1)	7	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)							Mis|N|F			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				---	---	---	---
ERCC5	2073	broad.mit.edu	37	13	103527712	103527712	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103527712C>T	uc001vpw.2	+	15	3463	c.3020C>T	c.(3019-3021)GCT>GTT	p.A1007V		NM_000123	NP_000114	P28715	ERCC5_HUMAN	XPG-complementing protein	1007	Interaction with PCNA.				negative regulation of apoptosis|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|response to UV-C|transcription-coupled nucleotide-excision repair|UV protection	nucleoplasm	bubble DNA binding|double-stranded DNA binding|endodeoxyribonuclease activity|metal ion binding|protein homodimerization activity|protein N-terminus binding|single-stranded DNA binding			ovary(4)|lung(1)|central_nervous_system(1)|skin(1)	7	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)							Mis|N|F			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				---	---	---	---
LIG4	3981	broad.mit.edu	37	13	108861650	108861650	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108861650G>C	uc001vqn.2	-	2	2240	c.1967C>G	c.(1966-1968)TCT>TGT	p.S656C	LIG4_uc001vqo.2_Missense_Mutation_p.S656C|LIG4_uc010agg.1_Missense_Mutation_p.S589C|LIG4_uc010agf.2_Missense_Mutation_p.S656C|LIG4_uc001vqp.2_Missense_Mutation_p.S656C	NM_002312	NP_002303	P49917	DNLI4_HUMAN	DNA ligase IV	656	BRCT 1.				cell cycle|cell division|cell proliferation|central nervous system development|chromosome organization|DNA ligation involved in DNA recombination|DNA ligation involved in DNA repair|DNA replication|double-strand break repair via nonhomologous end joining|in utero embryonic development|initiation of viral infection|isotype switching|negative regulation of neuron apoptosis|neuron apoptosis|nucleotide-excision repair, DNA gap filling|positive regulation of fibroblast proliferation|positive regulation of neurogenesis|pro-B cell differentiation|provirus integration|response to gamma radiation|response to X-ray|single strand break repair|somatic stem cell maintenance|T cell differentiation in thymus|T cell receptor V(D)J recombination	condensed chromosome|cytoplasm|DNA ligase IV complex|DNA-dependent protein kinase-DNA ligase 4 complex|focal adhesion|nucleoplasm	ATP binding|DNA binding|DNA ligase (ATP) activity|metal ion binding|protein C-terminus binding				0	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)												NHEJ					---	---	---	---
COL4A1	1282	broad.mit.edu	37	13	110839608	110839608	+	Silent	SNP	G	A	A	rs139448202		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110839608G>A	uc001vqw.3	-	25	1727	c.1605C>T	c.(1603-1605)TTC>TTT	p.F535F	COL4A1_uc010agl.2_Intron	NM_001845	NP_001836	P02462	CO4A1_HUMAN	alpha 1 type IV collagen preproprotein	535	Triple-helical region.				angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)															---	---	---	---
COL4A1	1282	broad.mit.edu	37	13	110850890	110850890	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110850890C>T	uc001vqw.3	-	21	1331	c.1209G>A	c.(1207-1209)CTG>CTA	p.L403L	COL4A1_uc010agl.2_Intron	NM_001845	NP_001836	P02462	CO4A1_HUMAN	alpha 1 type IV collagen preproprotein	403	Triple-helical region.				angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)															---	---	---	---
CARS2	79587	broad.mit.edu	37	13	111340065	111340065	+	Intron	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111340065T>C	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)													---	---	---	---
TEP1	7011	broad.mit.edu	37	14	20872766	20872766	+	Intron	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20872766A>G	uc001vxe.2	-						TEP1_uc010tlf.1_Intron|TEP1_uc010tlg.1_Intron	NM_007110	NP_009041			telomerase-associated protein 1						telomere maintenance via recombination	chromosome, telomeric region|cytoplasm|nuclear matrix|soluble fraction|telomerase holoenzyme complex	ATP binding|RNA binding			ovary(5)	5	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)														---	---	---	---
EDDM3B	64184	broad.mit.edu	37	14	21238529	21238529	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21238529T>C	uc001vyd.2	+	2	318	c.220T>C	c.(220-222)TAC>CAC	p.Y74H		NM_022360	NP_071755	P56851	EP3B_HUMAN	human epididymis-specific 3 beta precursor	74					spermatid development	extracellular region				ovary(1)	1																		---	---	---	---
TPPP2	122664	broad.mit.edu	37	14	21500085	21500085	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21500085C>T	uc001vzh.2	+	4	550	c.362C>T	c.(361-363)ACA>ATA	p.T121I	NDRG2_uc010tll.1_Intron	NM_173846	NP_776245	P59282	TPPP2_HUMAN	tubulin polymerization-promoting protein family	121						cytoplasm					0	all_cancers(95;0.000759)		OV - Ovarian serous cystadenocarcinoma(11;6.85e-11)|Epithelial(56;9.49e-09)|all cancers(55;3.84e-08)	GBM - Glioblastoma multiforme(265;0.0191)														---	---	---	---
SUPT16H	11198	broad.mit.edu	37	14	21820836	21820836	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21820836T>G	uc001wao.2	-	26	3479	c.3140A>C	c.(3139-3141)AAG>ACG	p.K1047T	SUPT16H_uc001wan.2_Missense_Mutation_p.K191T	NM_007192	NP_009123	Q9Y5B9	SP16H_HUMAN	chromatin-specific transcription elongation	1047					DNA repair|DNA replication|nucleosome disassembly|positive regulation of transcription elongation, DNA-dependent|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	chromosome|nucleoplasm	GTP binding				0	all_cancers(95;0.00115)		Epithelial(56;1.62e-06)|all cancers(55;1.49e-05)	GBM - Glioblastoma multiforme(265;0.0159)														---	---	---	---
DHRS4L2	317749	broad.mit.edu	37	14	24464255	24464255	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24464255T>C	uc001wli.3	+	3	451	c.321T>C	c.(319-321)CAT>CAC	p.H107H	DHRS4_uc001wlc.3_Intron|DHRS4L2_uc001wld.3_Intron|DHRS4L2_uc001wle.3_Intron|DHRS4L2_uc001wlg.3_RNA|DHRS4L2_uc001wlh.3_Intron|DHRS4L2_uc010tnt.1_Intron|DHRS4L2_uc010alb.2_5'UTR	NM_198083	NP_932349	D5KJA1	D5KJA1_HUMAN	dehydrogenase/reductase (SDR family) member 4	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment							binding|oxidoreductase activity			ovary(1)	1				GBM - Glioblastoma multiforme(265;0.00962)														---	---	---	---
CPNE6	9362	broad.mit.edu	37	14	24542730	24542730	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24542730G>A	uc001wll.2	+	3	290	c.191G>A	c.(190-192)CGC>CAC	p.R64H	CPNE6_uc010tnv.1_Missense_Mutation_p.R119H|CPNE6_uc001wlm.2_5'UTR|CPNE6_uc001wln.2_5'Flank	NM_006032	NP_006023	O95741	CPNE6_HUMAN	copine 6	64	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)														---	---	---	---
NOVA1	4857	broad.mit.edu	37	14	27064674	27064674	+	Silent	SNP	C	T	T	rs15844		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:27064674C>T	uc001wpy.2	-	2	540	c.222G>A	c.(220-222)CAG>CAA	p.Q74Q	NOVA1_uc001wpz.2_Silent_p.Q74Q|NOVA1_uc001wqa.2_5'UTR|NOVA1_uc001wqb.2_Silent_p.Q74Q	NM_002515	NP_002506	P51513	NOVA1_HUMAN	neuro-oncological ventral antigen 1 isoform 1	74	KH 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)														---	---	---	---
FOXG1	2290	broad.mit.edu	37	14	29237531	29237531	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29237531C>T	uc001wqe.2	+	1	1245	c.1046C>T	c.(1045-1047)TCG>TTG	p.S349L		NM_005249	NP_005240	P55316	FOXG1_HUMAN	forkhead box G1	349					axon midline choice point recognition|central nervous system neuron development|dorsal/ventral pattern formation|embryo development ending in birth or egg hatching|hindbrain development|inner ear morphogenesis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|nonmotile primary cilium assembly|nose development|positive regulation of cell cycle|positive regulation of neuroblast proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of mitotic cell cycle|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(2)|lung(2)	4			LUAD - Lung adenocarcinoma(48;0.011)|Lung(238;0.0575)	GBM - Glioblastoma multiforme(265;0.00413)														---	---	---	---
NPAS3	64067	broad.mit.edu	37	14	34266738	34266738	+	Silent	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34266738G>T	uc001wru.2	+	11	1441	c.1377G>T	c.(1375-1377)TCG>TCT	p.S459S	NPAS3_uc001wrs.2_Silent_p.S446S|NPAS3_uc001wrt.2_Silent_p.S427S|NPAS3_uc001wrv.2_Silent_p.S429S	NM_173159	NP_071406	Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3 isoform 3	459					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)														---	---	---	---
BAZ1A	11177	broad.mit.edu	37	14	35234378	35234378	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35234378A>G	uc001wsk.2	-	22	3966	c.3398T>C	c.(3397-3399)CTA>CCA	p.L1133P	BAZ1A_uc001wsl.2_Missense_Mutation_p.L1101P	NM_013448	NP_038476	Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	1133					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	35522473	35522473	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35522473C>T	uc001wsp.2	+						FAM177A1_uc001wsq.2_Intron	NM_001079519	NP_001072987			hypothetical protein LOC283635 isoform 2												0																		---	---	---	---
SSTR1	6751	broad.mit.edu	37	14	38679216	38679216	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38679216T>C	uc001wul.1	+	3	1239	c.622T>C	c.(622-624)TGC>CGC	p.C208R	SSTR1_uc010amu.1_Intron	NM_001049	NP_001040	P30872	SSR1_HUMAN	somatostatin receptor 1	208	Extracellular (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)													---	---	---	---
CLEC14A	161198	broad.mit.edu	37	14	38724486	38724486	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38724486C>A	uc001wum.1	-	1	1089	c.742G>T	c.(742-744)GGG>TGG	p.G248W		NM_175060	NP_778230	Q86T13	CLC14_HUMAN	C-type lectin domain family 14, member A	248	Extracellular (Potential).|EGF-like.					integral to membrane	sugar binding			ovary(3)|skin(1)	4	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;0.00439)														---	---	---	---
LRFN5	145581	broad.mit.edu	37	14	42355998	42355998	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42355998G>A	uc001wvm.2	+	3	1368	c.170G>A	c.(169-171)CGG>CAG	p.R57Q	LRFN5_uc010ana.2_Missense_Mutation_p.R57Q	NM_152447	NP_689660	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III	57	Extracellular (Potential).|LRR 1.					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)			---	---	---	---
LRFN5	145581	broad.mit.edu	37	14	42360530	42360530	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42360530C>T	uc001wvm.2	+	4	2661	c.1463C>T	c.(1462-1464)GCC>GTC	p.A488V	LRFN5_uc010ana.2_Intron	NM_152447	NP_689660	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III	488	Extracellular (Potential).|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)			---	---	---	---
KLHL28	54813	broad.mit.edu	37	14	45398324	45398324	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45398324A>G	uc001wvq.2	-	5	1869	c.1623T>C	c.(1621-1623)AAT>AAC	p.N541N	KLHL28_uc001wvr.2_Silent_p.N541N	NM_017658	NP_060128	Q9NXS3	KLH28_HUMAN	BTB (POZ) domain containing 5	541	Kelch 6.									ovary(1)	1																		---	---	---	---
FANCM	57697	broad.mit.edu	37	14	45642361	45642361	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45642361G>A	uc001wwd.3	+	13	2363	c.2264G>A	c.(2263-2265)TGC>TAC	p.C755Y	FANCM_uc010anf.2_Missense_Mutation_p.C729Y|FANCM_uc001wwe.3_Missense_Mutation_p.C291Y|FANCM_uc010ang.2_5'Flank	NM_020937	NP_065988	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	755					DNA repair	Fanconi anaemia nuclear complex	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|nuclease activity|protein binding			ovary(3)|lung(2)|breast(2)	7													Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
TRIM9	114088	broad.mit.edu	37	14	51489608	51489608	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51489608C>T	uc001wyx.3	-	3	1751	c.986G>A	c.(985-987)AGA>AAA	p.R329K	TRIM9_uc001wyy.2_Missense_Mutation_p.R329K|TRIM9_uc001wyz.3_Missense_Mutation_p.R329K	NM_015163	NP_055978	Q9C026	TRIM9_HUMAN	tripartite motif protein 9 isoform 1	329	Potential.				proteasomal ubiquitin-dependent protein catabolic process	cell junction|cytoskeleton|dendrite|synaptic vesicle	protein homodimerization activity|ubiquitin-protein ligase activity|zinc ion binding			skin(2)|lung(1)	3	all_epithelial(31;0.00418)|Breast(41;0.148)																	---	---	---	---
KTN1	3895	broad.mit.edu	37	14	56094714	56094714	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56094714G>A	uc001xcb.2	+	7	1350	c.1048G>A	c.(1048-1050)GCT>ACT	p.A350T	KTN1_uc001xce.2_Missense_Mutation_p.A350T|KTN1_uc001xcc.2_Missense_Mutation_p.A350T|KTN1_uc001xcd.2_Missense_Mutation_p.A350T|KTN1_uc010trb.1_Missense_Mutation_p.A350T|KTN1_uc001xcf.1_Missense_Mutation_p.A350T	NM_182926	NP_891556	Q86UP2	KTN1_HUMAN	kinectin 1 isoform a	350	Lumenal (Potential).|Potential.				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	56147397	56147397	+	Intron	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56147397A>G	uc001xcb.2	+						KTN1_uc001xce.2_Intron|KTN1_uc001xcc.2_Intron|KTN1_uc001xcd.2_Intron|KTN1_uc010trb.1_Intron|KTN1_uc001xcf.1_Intron|KTN1_uc010aoq.2_Intron|KTN1_uc010trc.1_Intron|KTN1_uc001xcg.2_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								---	---	---	---
EXOC5	10640	broad.mit.edu	37	14	57698411	57698411	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57698411G>A	uc001xct.2	-	11	1212	c.961C>T	c.(961-963)CTG>TTG	p.L321L	EXOC5_uc001xcs.2_5'UTR|EXOC5_uc010trg.1_Silent_p.L266L|EXOC5_uc010trh.1_Silent_p.L256L	NM_006544	NP_006535	O00471	EXOC5_HUMAN	SEC10 protein	321					exocytosis|post-Golgi vesicle-mediated transport|protein transport|vesicle docking	cytoplasm				ovary(2)|breast(1)	3																		---	---	---	---
SIX6	4990	broad.mit.edu	37	14	60976496	60976496	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60976496A>G	uc001xfa.3	+	1	559	c.380A>G	c.(379-381)GAC>GGC	p.D127G		NM_007374	NP_031400	O95475	SIX6_HUMAN	SIX homeobox 6	127					organ morphogenesis|visual perception	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0				OV - Ovarian serous cystadenocarcinoma(108;0.088)														---	---	---	---
SIX6	4990	broad.mit.edu	37	14	60976533	60976533	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60976533G>A	uc001xfa.3	+	1	596	c.417G>A	c.(415-417)ACG>ACA	p.T139T		NM_007374	NP_031400	O95475	SIX6_HUMAN	SIX homeobox 6	139	Homeobox.				organ morphogenesis|visual perception	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0				OV - Ovarian serous cystadenocarcinoma(108;0.088)														---	---	---	---
KCNH5	27133	broad.mit.edu	37	14	63269238	63269238	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63269238A>C	uc001xfx.2	-	9	1682	c.1631T>G	c.(1630-1632)GTT>GGT	p.V544G	KCNH5_uc001xfy.2_Missense_Mutation_p.V544G|KCNH5_uc001xfz.1_Missense_Mutation_p.V486G	NM_139318	NP_647479	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H,	544	Cytoplasmic (Potential).				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)														---	---	---	---
RHOJ	57381	broad.mit.edu	37	14	63671765	63671765	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63671765G>T	uc001xgb.1	+	1	621	c.178G>T	c.(178-180)GTT>TTT	p.V60F		NM_020663	NP_065714	Q9H4E5	RHOJ_HUMAN	ras homolog gene family, member J precursor	60					actin cytoskeleton organization|regulation of cell shape|regulation of small GTPase mediated signal transduction	cytosol|plasma membrane	GTP binding|GTPase activity				0				OV - Ovarian serous cystadenocarcinoma(108;0.00326)|all cancers(60;0.031)|BRCA - Breast invasive adenocarcinoma(234;0.119)														---	---	---	---
ZBTB1	22890	broad.mit.edu	37	14	64989844	64989844	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64989844A>G	uc001xhh.3	+	4	2053	c.1622A>G	c.(1621-1623)CAG>CGG	p.Q541R	ZBTB1_uc010aqg.2_Missense_Mutation_p.Q541R|ZBTB1_uc001xhi.2_Missense_Mutation_p.Q541R	NM_001123329	NP_001116801	Q9Y2K1	ZBTB1_HUMAN	zinc finger and BTB domain containing 1 isoform	541	C2H2-type 3; atypical.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1		all_lung(585;0.000567)|Myeloproliferative disorder(585;0.0255)|all_neural(303;0.0294)		UCEC - Uterine corpus endometrioid carcinoma (185;0.0182)|all cancers(60;3.78e-43)|OV - Ovarian serous cystadenocarcinoma(108;1.22e-20)|BRCA - Breast invasive adenocarcinoma(234;6.75e-06)|KIRC - Kidney renal clear cell carcinoma(182;0.00269)|STAD - Stomach adenocarcinoma(64;0.012)														---	---	---	---
C14orf50	145376	broad.mit.edu	37	14	65055011	65055011	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65055011G>A	uc001xhl.1	+	11	1176	c.1080G>A	c.(1078-1080)CCG>CCA	p.P360P	C14orf50_uc001xhm.1_Silent_p.P90P	NM_172365	NP_758953	Q96LQ0	CN050_HUMAN	hypothetical protein LOC145376	360										skin(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.00382)|all cancers(60;0.00427)|BRCA - Breast invasive adenocarcinoma(234;0.0488)														---	---	---	---
ZFYVE26	23503	broad.mit.edu	37	14	68252566	68252566	+	Intron	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68252566G>A	uc001xka.2	-						ZFYVE26_uc010tsz.1_Intron|ZFYVE26_uc001xkc.3_Intron	NM_015346	NP_056161			zinc finger, FYVE domain containing 26						cell cycle|cell death|cytokinesis|double-strand break repair via homologous recombination	centrosome|midbody	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			ovary(9)|breast(2)	11				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)														---	---	---	---
RGS6	9628	broad.mit.edu	37	14	72921228	72921228	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72921228C>T	uc001xna.3	+						RGS6_uc010ttn.1_Intron|RGS6_uc001xmx.3_Intron|RGS6_uc010tto.1_Intron|RGS6_uc001xmy.3_Intron|RGS6_uc010ttp.1_Intron|RGS6_uc010arg.2_Intron	NM_004296	NP_004287			regulator of G-protein signalling 6						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			upper_aerodigestive_tract(1)|lung(1)|skin(1)	3				all cancers(60;0.00309)|BRCA - Breast invasive adenocarcinoma(234;0.0281)|STAD - Stomach adenocarcinoma(64;0.0302)|OV - Ovarian serous cystadenocarcinoma(108;0.0476)														---	---	---	---
DCAF4	26094	broad.mit.edu	37	14	73420867	73420867	+	Intron	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73420867A>G	uc001xng.2	+						DCAF4_uc001xnj.2_Splice_Site_p.A270_splice|DCAF4_uc010ttr.1_Splice_Site_p.A248_splice|DCAF4_uc001xnh.2_Intron|DCAF4_uc010tts.1_Splice_Site_p.A209_splice|DCAF4_uc010ttt.1_Splice_Site_p.A55_splice|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																		---	---	---	---
ACOT1	641371	broad.mit.edu	37	14	74009849	74009849	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74009849C>T	uc001xol.1	+	3	954	c.756C>T	c.(754-756)GTC>GTT	p.V252V	HEATR4_uc010tua.1_Intron|ACOT1_uc010tuc.1_Intron	NM_001037161	NP_001032238	Q86TX2	ACOT1_HUMAN	acyl-CoA thioesterase 1	252					acyl-CoA metabolic process|long-chain fatty acid metabolic process|very long-chain fatty acid metabolic process	cytosol	carboxylesterase activity|palmitoyl-CoA hydrolase activity				0				OV - Ovarian serous cystadenocarcinoma(108;1.37e-45)|BRCA - Breast invasive adenocarcinoma(234;0.0033)														---	---	---	---
ACOT2	10965	broad.mit.edu	37	14	74040102	74040102	+	Silent	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74040102C>A	uc001xon.3	+	2	827	c.654C>A	c.(652-654)CCC>CCA	p.P218P	ACOT1_uc010tuc.1_Intron|ACOT2_uc001xom.2_Silent_p.P21P	NM_006821	NP_006812	P49753	ACOT2_HUMAN	acyl-CoA thioesterase 2	218					acyl-CoA metabolic process|long-chain fatty acid metabolic process|very long-chain fatty acid metabolic process	mitochondrion	carboxylesterase activity|palmitoyl-CoA hydrolase activity|protein binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.0033)|OV - Ovarian serous cystadenocarcinoma(108;0.0639)														---	---	---	---
ACOT2	10965	broad.mit.edu	37	14	74041707	74041707	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74041707C>T	uc001xon.3	+	3	1115	c.942C>T	c.(940-942)GTC>GTT	p.V314V	ACOT1_uc010tuc.1_Silent_p.V252V|ACOT2_uc001xom.2_Silent_p.V117V	NM_006821	NP_006812	P49753	ACOT2_HUMAN	acyl-CoA thioesterase 2	314					acyl-CoA metabolic process|long-chain fatty acid metabolic process|very long-chain fatty acid metabolic process	mitochondrion	carboxylesterase activity|palmitoyl-CoA hydrolase activity|protein binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.0033)|OV - Ovarian serous cystadenocarcinoma(108;0.0639)														---	---	---	---
C14orf43	91748	broad.mit.edu	37	14	74203839	74203839	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74203839G>A	uc001xot.2	-	3	2394	c.1611C>T	c.(1609-1611)GAC>GAT	p.D537D	C14orf43_uc001xou.2_Silent_p.D537D|C14orf43_uc010tud.1_Silent_p.D537D|C14orf43_uc010arw.2_RNA	NM_194278	NP_919254	Q6PJG2	CN043_HUMAN	hypothetical protein LOC91748	537					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(4)|central_nervous_system(1)	5				BRCA - Breast invasive adenocarcinoma(234;0.00358)|KIRC - Kidney renal clear cell carcinoma(182;0.0878)|OV - Ovarian serous cystadenocarcinoma(108;0.115)														---	---	---	---
C14orf115	55237	broad.mit.edu	37	14	74824922	74824922	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74824922C>T	uc001xpw.3	+	2	1627	c.1436C>T	c.(1435-1437)GCG>GTG	p.A479V		NM_018228	NP_060698	Q9H8Y1	VRTN_HUMAN	hypothetical protein LOC55237	479					transposition, DNA-mediated		DNA binding|transposase activity				0				BRCA - Breast invasive adenocarcinoma(234;0.00147)														---	---	---	---
NEK9	91754	broad.mit.edu	37	14	75570632	75570632	+	Silent	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75570632G>T	uc001xrl.2	-	14	1798	c.1644C>A	c.(1642-1644)ACC>ACA	p.T548T	NEK9_uc001xrk.2_Silent_p.T48T	NM_033116	NP_149107	Q8TD19	NEK9_HUMAN	NIMA-related kinase 9	548	RCC1 3.				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)														---	---	---	---
POMT2	29954	broad.mit.edu	37	14	77765074	77765074	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77765074G>A	uc001xti.2	-	8	1165	c.964C>T	c.(964-966)CGG>TGG	p.R322W	POMT2_uc001xth.1_Missense_Mutation_p.R20W	NM_013382	NP_037514	Q9UKY4	POMT2_HUMAN	protein-O-mannosyltransferase 2	322					protein O-linked glycosylation	endoplasmic reticulum membrane|integral to membrane	dolichyl-phosphate-mannose-protein mannosyltransferase activity|metal ion binding			ovary(1)	1			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0292)														---	---	---	---
GALC	2581	broad.mit.edu	37	14	88452926	88452926	+	Missense_Mutation	SNP	T	C	C	rs145580093	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88452926T>C	uc001xvt.2	-	4	748	c.349A>G	c.(349-351)ATG>GTG	p.M117V	GALC_uc010tvx.1_Missense_Mutation_p.M91V|GALC_uc010tvy.1_Missense_Mutation_p.M94V|GALC_uc010tvz.1_Missense_Mutation_p.M61V|GALC_uc001xvu.1_Missense_Mutation_p.M117V	NM_000153	NP_000144	P54803	GALC_HUMAN	galactosylceramidase isoform a precursor	117			M -> L (in GLD; adult).		carbohydrate metabolic process|galactosylceramide catabolic process	lysosome	cation binding|galactosylceramidase activity				0																		---	---	---	---
SERPINA11	256394	broad.mit.edu	37	14	94914785	94914785	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94914785T>G	uc001ydd.1	-	2	387	c.327A>C	c.(325-327)GAA>GAC	p.E109D		NM_001080451	NP_001073920	Q86U17	SPA11_HUMAN	serpin peptidase inhibitor, clade A (alpha-1	109					regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			kidney(1)	1				COAD - Colon adenocarcinoma(157;0.211)														---	---	---	---
DICER1	23405	broad.mit.edu	37	14	95593095	95593095	+	Intron	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95593095A>G	uc001ydw.2	-						DICER1_uc001ydv.2_Intron|DICER1_uc001ydx.2_Intron	NM_030621	NP_085124			dicer1						negative regulation of Schwann cell proliferation|negative regulation of transcription from RNA polymerase II promoter|nerve development|neuron projection morphogenesis|peripheral nervous system myelin formation|positive regulation of myelination|positive regulation of Schwann cell differentiation|pre-miRNA processing|production of siRNA involved in RNA interference|targeting of mRNA for destruction involved in RNA interference	cytosol|RNA-induced silencing complex	ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity			skin(2)|ovary(1)|pancreas(1)|lung(1)	5		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)				Mis F|N			pleuropulmonary blastoma			DICER_1_syndrome_|Familial_Multinodular_Goiter_				---	---	---	---
AK7	122481	broad.mit.edu	37	14	96922817	96922817	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96922817C>T	uc001yfn.2	+							NM_152327	NP_689540			adenylate kinase 7						cell projection organization	cytosol	adenylate kinase activity|ATP binding|cytidylate kinase activity			ovary(1)	1		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)														---	---	---	---
CYP46A1	10858	broad.mit.edu	37	14	100182306	100182306	+	Intron	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100182306G>A	uc001ygo.2	+						CYP46A1_uc001ygp.2_Intron	NM_006668	NP_006659			cytochrome P450, family 46						bile acid biosynthetic process|cholesterol catabolic process|nervous system development|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	cholesterol 24-hydroxylase activity|electron carrier activity|heme binding|steroid hydroxylase activity				0		Melanoma(154;0.0866)|all_epithelial(191;0.179)																---	---	---	---
DYNC1H1	1778	broad.mit.edu	37	14	102445718	102445718	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102445718G>A	uc001yks.2	+	3	571	c.407G>A	c.(406-408)CGG>CAG	p.R136Q		NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1	136	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	102482798	102482798	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102482798C>T	uc001yks.2	+	37	7750	c.7586C>T	c.(7585-7587)GCG>GTG	p.A2529V	DYNC1H1_uc001ykt.1_Missense_Mutation_p.A20V	NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1	2529					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																		---	---	---	---
BRF1	2972	broad.mit.edu	37	14	105688235	105688235	+	Silent	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105688235G>T	uc001yqp.2	-	11	1428	c.1065C>A	c.(1063-1065)ACC>ACA	p.T355T	BRF1_uc010tyo.1_Silent_p.T240T|BRF1_uc010typ.1_Silent_p.T240T|BRF1_uc001yqk.2_5'UTR|BRF1_uc001yql.2_Silent_p.T151T|BRF1_uc001yqo.2_Silent_p.T117T|BRF1_uc010axg.1_Silent_p.T328T|BRF1_uc001yqn.2_Intron|BRF1_uc010axh.1_Intron|BRF1_uc010axi.1_5'UTR	NM_001519	NP_001510	Q92994	TF3B_HUMAN	transcription initiation factor IIIB isoform 1	355					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)														---	---	---	---
OR4N4	283694	broad.mit.edu	37	15	22382633	22382633	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22382633G>T	uc001yuc.1	+	7	1142	c.161G>T	c.(160-162)GGG>GTG	p.G54V	LOC727924_uc001yub.1_RNA|OR4N4_uc010tzv.1_Missense_Mutation_p.G54V	NM_001005241	NP_001005241	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N,	54	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(4)|skin(1)	5		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)														---	---	---	---
NDN	4692	broad.mit.edu	37	15	23931514	23931514	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23931514T>C	uc001ywk.2	-	1	937	c.851A>G	c.(850-852)AAG>AGG	p.K284R		NM_002487	NP_002478	Q99608	NECD_HUMAN	necdin	284	MAGE.				negative regulation of cell proliferation|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perikaryon	DNA binding				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;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00179)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)										Prader-Willi_syndrome				---	---	---	---
SNRPN	6638	broad.mit.edu	37	15	25223440	25223440	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25223440G>A	uc001ywp.1	+	12	1550	c.660G>A	c.(658-660)ATG>ATA	p.M220I	SNRPN_uc001ywq.1_Missense_Mutation_p.M220I|SNRPN_uc001ywr.1_Missense_Mutation_p.M220I|SNRPN_uc001yws.1_Missense_Mutation_p.M220I|SNRPN_uc001ywt.1_Missense_Mutation_p.M220I|SNRPN_uc001ywv.1_Missense_Mutation_p.M223I|SNRPN_uc001yww.1_Missense_Mutation_p.M220I|SNRPN_uc001ywx.1_Missense_Mutation_p.M220I|SNRPN_uc001ywz.1_RNA|PAR-SN_uc001yxa.1_Intron|SNRPN_uc001ywy.1_3'UTR	NM_022807	NP_073718	P63162	RSMN_HUMAN	small nuclear ribonucleoprotein polypeptide N	220	Repeat-rich region.|				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	25490664	25490664	+	Intron	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25490664T>C	uc001zae.2	+						SNORD115-41_uc001zaj.1_RNA|SNORD115-10_uc001zak.1_5'Flank					Homo sapiens clone Rt-16 SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced.																														---	---	---	---
ATP10A	57194	broad.mit.edu	37	15	25926036	25926036	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25926036A>G	uc010ayu.2	-	19	3705	c.3599T>C	c.(3598-3600)CTG>CCG	p.L1200P		NM_024490	NP_077816	O60312	AT10A_HUMAN	ATPase, class V, type 10A	1200	Helical; (Potential).				ATP biosynthetic process|regulation of cell shape	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			pancreas(2)|ovary(1)|breast(1)|liver(1)	5		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)														---	---	---	---
HERC2	8924	broad.mit.edu	37	15	28437159	28437159	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28437159C>T	uc001zbj.2	-	53	8505	c.8399G>A	c.(8398-8400)CGT>CAT	p.R2800H	HERC2_uc001zbk.1_Missense_Mutation_p.R335H	NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	2800	DOC.				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)												OREG0022997	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TRPM1	4308	broad.mit.edu	37	15	31294831	31294831	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31294831G>T	uc001zfm.2	-	27	4134	c.4006C>A	c.(4006-4008)CCA>ACA	p.P1336T	TRPM1_uc010azy.2_Missense_Mutation_p.P1243T|TRPM1_uc001zfl.2_RNA	NM_002420	NP_002411	Q7Z4N2	TRPM1_HUMAN	transient receptor potential cation channel,	1336	Cytoplasmic (Potential).				cellular response to light stimulus|visual perception	integral to plasma membrane	calcium channel activity|receptor activity			ovary(2)|pancreas(1)|skin(1)	4		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)														---	---	---	---
ARHGAP11A	9824	broad.mit.edu	37	15	32926217	32926217	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32926217A>G	uc001zgy.1	+	10	2041	c.1319A>G	c.(1318-1320)AAT>AGT	p.N440S	ARHGAP11A_uc010ubw.1_Missense_Mutation_p.N251S|ARHGAP11A_uc001zgw.2_Missense_Mutation_p.N440S|ARHGAP11A_uc001zgx.2_Missense_Mutation_p.N412S|ARHGAP11A_uc010ubx.1_Missense_Mutation_p.N251S	NM_014783	NP_055598	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A isoform 1	440					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			skin(3)|breast(2)|urinary_tract(1)	6		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)														---	---	---	---
RYR3	6263	broad.mit.edu	37	15	33765622	33765622	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33765622G>T	uc001zhi.2	+	2	124	c.54G>T	c.(52-54)GAG>GAT	p.E18D	RYR3_uc010bar.2_Missense_Mutation_p.E18D	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	18	Cytoplasmic (By similarity).				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)														---	---	---	---
FAM98B	283742	broad.mit.edu	37	15	38756385	38756385	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38756385C>T	uc001zkb.1	+						FAM98B_uc001zkc.2_Intron	NM_001042429	NP_001035894			family with sequence similarity 98, member B							tRNA-splicing ligase complex	protein binding			ovary(1)	1		all_cancers(109;3.11e-17)|all_epithelial(112;2.64e-15)|Lung NSC(122;2.11e-11)|all_lung(180;5.61e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;9e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0209)														---	---	---	---
GPR176	11245	broad.mit.edu	37	15	40094085	40094085	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40094085C>T	uc001zkj.1	-	3	1662	c.796G>A	c.(796-798)GCC>ACC	p.A266T	GPR176_uc010uck.1_Missense_Mutation_p.A206T	NM_007223	NP_009154	Q14439	GP176_HUMAN	G protein-coupled receptor 176	266	Cytoplasmic (Potential).				synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity			ovary(2)|skin(2)|pancreas(1)|central_nervous_system(1)	6		all_cancers(109;4.05e-15)|all_epithelial(112;2.96e-13)|Lung NSC(122;8.53e-11)|all_lung(180;2.71e-09)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;4.4e-06)|BRCA - Breast invasive adenocarcinoma(123;0.123)												OREG0023053	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PLCB2	5330	broad.mit.edu	37	15	40587214	40587214	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40587214A>G	uc001zld.2	-	18	2130	c.1829T>C	c.(1828-1830)ATG>ACG	p.M610T	PLCB2_uc010bbo.2_Missense_Mutation_p.M606T|PLCB2_uc010ucm.1_Missense_Mutation_p.M610T	NM_004573	NP_004564	Q00722	PLCB2_HUMAN	phospholipase C, beta 2	610	PI-PLC Y-box.				activation of phospholipase C activity|intracellular signal transduction|lipid catabolic process|phospholipid metabolic process|synaptic transmission	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(3)|breast(3)|kidney(1)|pancreas(1)	8		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)														---	---	---	---
SPINT1	6692	broad.mit.edu	37	15	41146067	41146067	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41146067C>T	uc001zna.2	+	5	1105	c.901C>T	c.(901-903)CGG>TGG	p.R301W	SPINT1_uc001znb.2_Missense_Mutation_p.R301W|SPINT1_uc001znc.2_Missense_Mutation_p.R301W|SPINT1_uc010ucs.1_Missense_Mutation_p.R301W	NM_181642	NP_857593	O43278	SPIT1_HUMAN	serine peptidase inhibitor, Kunitz type 1	301						extracellular region|membrane fraction	protein binding|serine-type endopeptidase inhibitor activity			ovary(1)	1		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)														---	---	---	---
LTK	4058	broad.mit.edu	37	15	41805025	41805025	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41805025C>A	uc001zoa.3	-	3	417	c.239G>T	c.(238-240)GGG>GTG	p.G80V	LTK_uc001zob.3_Missense_Mutation_p.G80V|LTK_uc010ucx.1_Missense_Mutation_p.G80V|LTK_uc010bcg.2_Intron	NM_002344	NP_002335	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase isoform 1	80	Extracellular (Potential).				apoptosis|cell proliferation|phosphatidylinositol 3-kinase cascade|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane|soluble fraction	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(6)|central_nervous_system(1)	7		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)											TSP Lung(18;0.14)			---	---	---	---
MGA	23269	broad.mit.edu	37	15	42042288	42042288	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42042288G>A	uc010ucy.1	+	17	6664	c.6483G>A	c.(6481-6483)AAG>AAA	p.K2161K	MGA_uc010ucz.1_Silent_p.K1952K|MGA_uc010uda.1_Silent_p.K777K|MGA_uc001zoi.2_Silent_p.K375K	NM_001164273	NP_001157745	Q8IWI9	MGAP_HUMAN	MAX-interacting protein isoform 1	2122	Basic motif.					MLL1 complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	12		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)														---	---	---	---
MGA	23269	broad.mit.edu	37	15	42058341	42058341	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42058341C>T	uc010ucy.1	+	24	8242	c.8061C>T	c.(8059-8061)ACC>ACT	p.T2687T	MGA_uc010ucz.1_Silent_p.T2478T	NM_001164273	NP_001157745	Q8IWI9	MGAP_HUMAN	MAX-interacting protein isoform 1	2648						MLL1 complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	12		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)														---	---	---	---
SPTBN5	51332	broad.mit.edu	37	15	42175659	42175659	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42175659G>A	uc001zos.2	-	8	1774	c.1441C>T	c.(1441-1443)CAG>TAG	p.Q481*		NM_016642	NP_057726	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	516	Spectrin 2.				actin cytoskeleton organization|actin filament capping|axon guidance	cytosol|membrane|spectrin				ovary(1)|central_nervous_system(1)	2		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)														---	---	---	---
SPTBN5	51332	broad.mit.edu	37	15	42180164	42180164	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42180164G>A	uc001zos.2	-	5	849	c.516C>T	c.(514-516)AGC>AGT	p.S172S		NM_016642	NP_057726	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	207	Actin-binding.|CH 2.				actin cytoskeleton organization|actin filament capping|axon guidance	cytosol|membrane|spectrin				ovary(1)|central_nervous_system(1)	2		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)														---	---	---	---
EHD4	30844	broad.mit.edu	37	15	42211572	42211572	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42211572G>A	uc001zot.2	-	4	823	c.760C>T	c.(760-762)CGC>TGC	p.R254C		NM_139265	NP_644670	Q9H223	EHD4_HUMAN	EH-domain containing 4	254					endocytic recycling|protein homooligomerization	early endosome membrane|endoplasmic reticulum|nucleus|recycling endosome membrane	ATP binding|calcium ion binding|GTP binding|GTPase activity|nucleic acid binding|protein binding			ovary(2)	2		all_cancers(109;2.54e-12)|all_epithelial(112;6.59e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)		OV - Ovarian serous cystadenocarcinoma(18;1.6e-19)|GBM - Glioblastoma multiforme(94;3.77e-06)|COAD - Colon adenocarcinoma(120;0.0474)|Colorectal(105;0.0538)														---	---	---	---
TTBK2	146057	broad.mit.edu	37	15	43075687	43075687	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43075687C>T	uc001zqo.2	-	11	1566	c.1127G>A	c.(1126-1128)CGT>CAT	p.R376H	TTBK2_uc010bcy.2_Missense_Mutation_p.R307H|TTBK2_uc001zqp.2_Missense_Mutation_p.R376H|TTBK2_uc010bcz.1_Missense_Mutation_p.R341H	NM_173500	NP_775771	Q6IQ55	TTBK2_HUMAN	tau tubulin kinase 2	376					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)														---	---	---	---
DUOX2	50506	broad.mit.edu	37	15	45402159	45402159	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45402159G>A	uc010bea.2	-	10	1263	c.1060C>T	c.(1060-1062)CGG>TGG	p.R354W	DUOX2_uc001zun.2_Missense_Mutation_p.R354W	NM_014080	NP_054799	Q9NRD8	DUOX2_HUMAN	dual oxidase 2 precursor	354	Extracellular (Potential).|Peroxidase-like; mediates peroxidase activity (By similarity).				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)														---	---	---	---
SHC4	399694	broad.mit.edu	37	15	49255019	49255019	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49255019G>T	uc001zxb.1	-	1	623	c.194C>A	c.(193-195)CCT>CAT	p.P65H		NM_203349	NP_976224	Q6S5L8	SHC4_HUMAN	rai-like protein	65	CH2.				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)														---	---	---	---
HDC	3067	broad.mit.edu	37	15	50534788	50534788	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50534788A>G	uc001zxz.2	-	12	1764	c.1658T>C	c.(1657-1659)TTT>TCT	p.F553S	HDC_uc001zxy.2_Missense_Mutation_p.F296S|HDC_uc010uff.1_Missense_Mutation_p.F520S	NM_002112	NP_002103	P19113	DCHS_HUMAN	histidine decarboxylase	553					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)													---	---	---	---
HDC	3067	broad.mit.edu	37	15	50544819	50544819	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50544819T>G	uc001zxz.2	-	8	1046	c.940A>C	c.(940-942)ACT>CCT	p.T314P	HDC_uc001zxy.2_Missense_Mutation_p.T57P|HDC_uc010uff.1_Missense_Mutation_p.T314P	NM_002112	NP_002103	P19113	DCHS_HUMAN	histidine decarboxylase	314					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)													---	---	---	---
HDC	3067	broad.mit.edu	37	15	50546391	50546391	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50546391A>G	uc001zxz.2	-	6	762	c.656T>C	c.(655-657)CTC>CCC	p.L219P	HDC_uc001zxy.2_5'Flank|HDC_uc010uff.1_Missense_Mutation_p.L219P|HDC_uc010bet.1_Missense_Mutation_p.L140P|HDC_uc010beu.1_Missense_Mutation_p.L219P	NM_002112	NP_002103	P19113	DCHS_HUMAN	histidine decarboxylase	219					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)													---	---	---	---
AP4E1	23431	broad.mit.edu	37	15	51294833	51294833	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51294833T>C	uc001zyx.1	+	21	3418	c.3388T>C	c.(3388-3390)TGT>CGT	p.C1130R	AP4E1_uc010bex.1_RNA	NM_007347	NP_031373	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1	1130					intracellular protein transport|vesicle-mediated transport	COPI vesicle coat	binding|structural molecule activity				0				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)														---	---	---	---
DMXL2	23312	broad.mit.edu	37	15	51780254	51780254	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51780254C>T	uc002abf.2	-	22	5339	c.5114G>A	c.(5113-5115)CGA>CAA	p.R1705Q	DMXL2_uc010ufy.1_Missense_Mutation_p.R1705Q|DMXL2_uc010bfa.2_Missense_Mutation_p.R1069Q	NM_015263	NP_056078	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	1705						cell junction|synaptic vesicle membrane	Rab GTPase binding			ovary(6)|skin(3)	9				all cancers(107;0.00494)														---	---	---	---
MYO5A	4644	broad.mit.edu	37	15	52613593	52613593	+	Silent	SNP	G	A	A	rs56219052		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52613593G>A	uc002aby.2	-	37	5083	c.4839C>T	c.(4837-4839)CTC>CTT	p.L1613L	MYO5A_uc002abx.3_Silent_p.L1586L|MYO5A_uc010ugd.1_Silent_p.L335L	NM_000259	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA isoform 1	1613	Dilute.				actin filament-based movement|transport	cytoplasm|growth cone|myosin complex|ruffle	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|central_nervous_system(1)	4				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)														---	---	---	---
UNC13C	440279	broad.mit.edu	37	15	54542430	54542430	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54542430A>C	uc002ack.2	+	6	3236	c.3236A>C	c.(3235-3237)CAC>CCC	p.H1079P		NM_001080534	NP_001074003	Q8NB66	UN13C_HUMAN	unc-13 homolog C	1079					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)														---	---	---	---
RFX7	64864	broad.mit.edu	37	15	56385781	56385781	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56385781C>A	uc010bfn.2	-	9	4145	c.4145G>T	c.(4144-4146)AGC>ATC	p.S1382I	RFX7_uc010ugk.1_Intron|RFX7_uc002adn.1_Intron	NM_022841	NP_073752	Q2KHR2	RFX7_HUMAN	regulatory factor X domain containing 2	1285					regulation of transcription, DNA-dependent	nucleus	DNA binding				0																		---	---	---	---
DAPK2	23604	broad.mit.edu	37	15	64231561	64231561	+	Splice_Site	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64231561C>T	uc002amr.2	-	5	485	c.454_splice	c.e5-1	p.P152_splice	DAPK2_uc010uim.1_Splice_Site|DAPK2_uc010bgu.1_Splice_Site_p.P142_splice	NM_014326	NP_055141			death-associated kinase 2						apoptosis|induction of apoptosis|intracellular protein kinase cascade	cytoplasm	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity|identical protein binding			stomach(1)|central_nervous_system(1)	2				LUAD - Lung adenocarcinoma(2;0.215)														---	---	---	---
ANKDD1A	348094	broad.mit.edu	37	15	65239637	65239637	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65239637A>C	uc002aoa.2	+	13	1204	c.1175A>C	c.(1174-1176)GAT>GCT	p.D392A	ANKDD1A_uc002aoc.2_RNA|ANKDD1A_uc010bha.2_Missense_Mutation_p.D269A	NM_182703	NP_874362	Q495B1	AKD1A_HUMAN	ankyrin repeat and death domain containing 1A	392					signal transduction					ovary(1)	1																		---	---	---	---
RAB11A	8766	broad.mit.edu	37	15	66169843	66169843	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66169843C>T	uc002apk.2	+	2	342	c.214C>T	c.(214-216)CGA>TGA	p.R72*	RAB11A_uc010ujk.1_Nonsense_Mutation_p.R72*	NM_004663	NP_004654	P62491	RB11A_HUMAN	Ras-related protein Rab-11A	72					cell cycle|cytokinesis|neuron projection development|plasma membrane to endosome transport|protein localization in plasma membrane|small GTPase mediated signal transduction|vesicle-mediated transport	cleavage furrow|plasma membrane|recycling endosome membrane|trans-Golgi network	GTP binding|GTPase activity|syntaxin binding				0																		---	---	---	---
CALML4	91860	broad.mit.edu	37	15	68489868	68489868	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68489868T>A	uc002arb.2	-	4	1137	c.403A>T	c.(403-405)ATG>TTG	p.M135L	CALML4_uc002arc.2_Missense_Mutation_p.M88L|CALML4_uc002ard.2_RNA|CALML4_uc002are.2_RNA|CALML4_uc010bhz.2_Intron	NM_033429	NP_219501	Q96GE6	CALL4_HUMAN	calmodulin-like 4 isoform 1	135	EF-hand 3.						calcium ion binding				0																		---	---	---	---
FEM1B	10116	broad.mit.edu	37	15	68582761	68582761	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68582761G>A	uc002arg.2	+	2	1680	c.1065G>A	c.(1063-1065)GCG>GCA	p.A355A	FEM1B_uc002arh.2_Silent_p.A275A	NM_015322	NP_056137	Q9UK73	FEM1B_HUMAN	fem-1 homolog b	355	TPR.				apoptosis|induction of apoptosis|regulation of DNA damage checkpoint|regulation of ubiquitin-protein ligase activity	cytoplasm|nucleus	death receptor binding|ubiquitin-protein ligase activity				0																		---	---	---	---
KIF23	9493	broad.mit.edu	37	15	69727982	69727982	+	Intron	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69727982T>C	uc002asb.2	+						KIF23_uc002asc.2_Intron|KIF23_uc010bii.2_Intron|KIF23_uc010ukc.1_Intron|KIF23_uc010bih.1_Intron	NM_138555	NP_612565			kinesin family member 23 isoform 1						blood coagulation|cytokinesis|microtubule-based movement|mitosis|mitotic spindle elongation	cytosol|kinesin complex|microtubule|midbody|nucleoplasm|spindle	ATP binding|microtubule motor activity|protein binding				0																		---	---	---	---
THSD4	79875	broad.mit.edu	37	15	72039251	72039251	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72039251G>T	uc002atb.1	+	12	2190	c.2111G>T	c.(2110-2112)CGC>CTC	p.R704L	THSD4_uc002ate.2_Missense_Mutation_p.R344L	NM_024817	NP_079093	Q6ZMP0	THSD4_HUMAN	thrombospondin, type I, domain containing 4	704	TSP type-1 2.					proteinaceous extracellular matrix	metalloendopeptidase activity			ovary(2)	2																		---	---	---	---
NEO1	4756	broad.mit.edu	37	15	73590878	73590878	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73590878T>C	uc002avm.3	+	27	4233	c.4091T>C	c.(4090-4092)GTG>GCG	p.V1364A	NEO1_uc010ukx.1_Missense_Mutation_p.V1353A|NEO1_uc010uky.1_Missense_Mutation_p.V1311A|NEO1_uc010ukz.1_Missense_Mutation_p.V777A|NEO1_uc002avn.3_Missense_Mutation_p.V1002A	NM_002499	NP_002490	Q92859	NEO1_HUMAN	neogenin homolog 1 precursor	1364	Cytoplasmic (Potential).				axon guidance|cell adhesion|positive regulation of muscle cell differentiation	Golgi apparatus|integral to plasma membrane|nucleus				pancreas(1)	1																		---	---	---	---
CYP1A1	1543	broad.mit.edu	37	15	75015122	75015122	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75015122C>T	uc002ayp.3	-	2	439	c.317G>A	c.(316-318)CGG>CAG	p.R106Q	CYP1A1_uc010bjv.2_RNA|CYP1A1_uc010bjw.2_RNA|CYP1A1_uc010bju.2_Intron|CYP1A1_uc010bjx.2_Intron|CYP1A1_uc002ayq.3_Missense_Mutation_p.R106Q|CYP1A1_uc010bjy.2_Missense_Mutation_p.R106Q|CYP1A1_uc010bjz.1_Intron	NM_000499	NP_000490	P04798	CP1A1_HUMAN	cytochrome P450, family 1, subfamily A,	106					cellular lipid metabolic process|drug metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding|vitamin D 24-hydroxylase activity			ovary(2)|breast(2)|pancreas(1)	5					Arsenic trioxide(DB01169)|Benzphetamine(DB00865)|Bleomycin(DB00290)|Chlorzoxazone(DB00356)|Dacarbazine(DB00851)|Dactinomycin(DB00970)|Esomeprazole(DB00736)|Estrone(DB00655)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Ginseng(DB01404)|Granisetron(DB00889)|Ketoconazole(DB01026)|Menadione(DB00170)|Picrotoxin(DB00466)|Primaquine(DB01087)|Quinidine(DB00908)|Quinine(DB00468)|Thiabendazole(DB00730)									Endometrial_Cancer_Familial_Clustering_of|ACTH-independent_macronodular_adrenal_hyperplasia				---	---	---	---
C15orf39	56905	broad.mit.edu	37	15	75498793	75498793	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75498793G>A	uc002azp.3	+	2	724	c.404G>A	c.(403-405)CGC>CAC	p.R135H	C15orf39_uc002azq.3_Missense_Mutation_p.R135H|C15orf39_uc002azr.3_5'Flank	NM_015492	NP_056307	Q6ZRI6	CO039_HUMAN	hypothetical protein LOC56905	135											0																		---	---	---	---
BCL2A1	597	broad.mit.edu	37	15	80263339	80263339	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80263339C>T	uc002bfc.3	-	1	305	c.123G>A	c.(121-123)GCG>GCA	p.A41A	BCL2A1_uc002bfd.3_Silent_p.A41A	NM_004049	NP_004040	Q16548	B2LA1_HUMAN	BCL2-related protein A1 isoform 1	41					anti-apoptosis|apoptosis	cytoplasm	protein binding			pancreas(1)	1																		---	---	---	---
KIAA1199	57214	broad.mit.edu	37	15	81212446	81212446	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81212446T>C	uc002bfw.1	+	14	2069	c.1809T>C	c.(1807-1809)GTT>GTC	p.V603V	KIAA1199_uc010unn.1_Silent_p.V603V	NM_018689	NP_061159	Q8WUJ3	K1199_HUMAN	KIAA1199 precursor	603	PbH1 2.									upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3																		---	---	---	---
AP3B2	8120	broad.mit.edu	37	15	83328374	83328374	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83328374T>C	uc010uoh.1	-	26	3364	c.3187A>G	c.(3187-3189)AGC>GGC	p.S1063G	AP3B2_uc010uoi.1_Missense_Mutation_p.S1082G|AP3B2_uc010uoj.1_Missense_Mutation_p.S1031G|AP3B2_uc010bmp.2_Missense_Mutation_p.S126G|AP3B2_uc010uog.1_Missense_Mutation_p.S699G	NM_004644	NP_004635	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2	1063					endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport	clathrin coated vesicle membrane|COPI-coated vesicle|membrane coat	binding|protein transporter activity			ovary(3)|breast(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(143;0.229)															---	---	---	---
BNC1	646	broad.mit.edu	37	15	83933011	83933011	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83933011T>G	uc002bjt.1	-	4	1080	c.992A>C	c.(991-993)AAG>ACG	p.K331T	BNC1_uc010uos.1_Missense_Mutation_p.K319T	NM_001717	NP_001708	Q01954	BNC1_HUMAN	basonuclin 1	331					epidermis development|positive regulation of cell proliferation	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3																		---	---	---	---
ALPK3	57538	broad.mit.edu	37	15	85400990	85400990	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85400990T>C	uc002ble.2	+	6	3794	c.3627T>C	c.(3625-3627)AGT>AGC	p.S1209S		NM_020778	NP_065829	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1209					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)															---	---	---	---
AGBL1	123624	broad.mit.edu	37	15	86807860	86807860	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86807860T>C	uc002blz.1	+	10	1400	c.1320T>C	c.(1318-1320)ACT>ACC	p.T440T	AGBL1_uc002bma.1_Silent_p.T171T|AGBL1_uc002bmb.1_Silent_p.T134T	NM_152336	NP_689549	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	440					C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0																		---	---	---	---
AEN	64782	broad.mit.edu	37	15	89169707	89169707	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89169707C>T	uc002bmt.2	+	2	418	c.267C>T	c.(265-267)GGC>GGT	p.G89G	AEN_uc010bnl.2_Silent_p.G89G|AEN_uc010bnm.1_Silent_p.G89G	NM_022767	NP_073604	Q8WTP8	AEN_HUMAN	interferon stimulated exonuclease gene	89					apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|response to ionizing radiation	nucleolus|nucleoplasm	exonuclease activity|nucleic acid binding				0																		---	---	---	---
POLG	5428	broad.mit.edu	37	15	89860001	89860001	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89860001C>T	uc002bns.3	-	23	3983	c.3701G>A	c.(3700-3702)CGA>CAA	p.R1234Q	FANCI_uc010bnp.1_3'UTR|FANCI_uc002bnm.1_3'UTR|FANCI_uc002bnn.1_RNA|FANCI_uc002bnp.1_3'UTR|FANCI_uc002bnq.1_3'UTR|POLG_uc002bnr.3_Missense_Mutation_p.R1234Q	NM_002693	NP_002684	P54098	DPOG1_HUMAN	DNA-directed DNA polymerase gamma	1234					base-excision repair, gap-filling|cell death|DNA-dependent DNA replication	mitochondrial nucleoid	DNA binding|DNA-directed DNA polymerase activity|protease binding			ovary(1)|lung(1)	2	Lung NSC(78;0.0472)|all_lung(78;0.089)		STAD - Stomach adenocarcinoma(125;0.165)										DNA_polymerases_(catalytic_subunits)					---	---	---	---
IDH2	3418	broad.mit.edu	37	15	90630409	90630409	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90630409G>A	uc002box.2	-	7	988	c.902C>T	c.(901-903)TCG>TTG	p.S301L	IDH2_uc010uqb.1_Missense_Mutation_p.S249L|IDH2_uc010uqc.1_Missense_Mutation_p.S171L|IDH2_uc010bnu.2_Missense_Mutation_p.S192L	NM_002168	NP_002159	P48735	IDHP_HUMAN	isocitrate dehydrogenase 2 (NADP+),	301					2-oxoglutarate metabolic process|glyoxylate cycle|isocitrate metabolic process|tricarboxylic acid cycle	mitochondrial matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding			haematopoietic_and_lymphoid_tissue(621)|central_nervous_system(80)|bone(7)|skin(3)	711	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106)					M		GBM						OREG0023466	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ZNF774	342132	broad.mit.edu	37	15	90903588	90903588	+	Silent	SNP	C	T	T	rs139630850		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90903588C>T	uc002bpk.3	+	4	711	c.525C>T	c.(523-525)GGC>GGT	p.G175G		NM_001004309	NP_001004309	Q6NX45	ZN774_HUMAN	zinc finger protein 774	175					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Melanoma(11;0.00551)|Lung NSC(78;0.0158)|all_lung(78;0.0331)		BRCA - Breast invasive adenocarcinoma(143;0.0224)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)															---	---	---	---
BLM	641	broad.mit.edu	37	15	91304139	91304139	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91304139A>G	uc002bpr.2	+	7	1633	c.1536A>G	c.(1534-1536)GGA>GGG	p.G512G	BLM_uc010uqh.1_Silent_p.G512G|BLM_uc010uqi.1_Silent_p.G137G|BLM_uc010bnx.2_Silent_p.G512G|BLM_uc002bps.1_Silent_p.G74G	NM_000057	NP_000048	P54132	BLM_HUMAN	Bloom syndrome protein	512					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				---	---	---	---
MAN2A2	4122	broad.mit.edu	37	15	91453336	91453336	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91453336T>G	uc010bnz.2	+	10	1506	c.1391T>G	c.(1390-1392)CTT>CGT	p.L464R	MAN2A2_uc010boa.2_Missense_Mutation_p.L506R|MAN2A2_uc002bqc.2_Missense_Mutation_p.L464R|MAN2A2_uc010uql.1_Intron|MAN2A2_uc010uqm.1_Intron|MAN2A2_uc010uqn.1_5'Flank	NM_006122	NP_006113	P49641	MA2A2_HUMAN	mannosidase, alpha, class 2A, member 2	464	Lumenal (Potential).				mannose metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-mannosidase activity|carbohydrate binding|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity|zinc ion binding			large_intestine(2)|ovary(1)	3	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)															---	---	---	---
RCCD1	91433	broad.mit.edu	37	15	91503700	91503700	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91503700T>C	uc002bqj.2	+	7	1201	c.921T>C	c.(919-921)TGT>TGC	p.C307C	RCCD1_uc002bqk.2_Silent_p.C307C|RCCD1_uc002bql.2_Silent_p.C305C|RCCD1_uc010bob.2_Silent_p.C96C	NM_033544	NP_291022	A6NED2	RCCD1_HUMAN	RCC1 domain containing 1	307	RCC1 3.										0	Lung NSC(78;0.0987)|all_lung(78;0.175)		Lung(145;0.189)															---	---	---	---
LRRK1	79705	broad.mit.edu	37	15	101593198	101593198	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101593198G>A	uc002bwr.2	+	25	4080	c.3761G>A	c.(3760-3762)GGC>GAC	p.G1254D	LRRK1_uc010usb.1_RNA|LRRK1_uc010usc.1_RNA|LRRK1_uc002bws.2_5'Flank	NM_024652	NP_078928	Q38SD2	LRRK1_HUMAN	leucine-rich repeat kinase 1	1254	ATP (By similarity).|Protein kinase.				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)															---	---	---	---
RHOT2	89941	broad.mit.edu	37	16	720295	720295	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:720295A>G	uc002cip.2	+	7	443	c.376A>G	c.(376-378)AGC>GGC	p.S126G	RHOT2_uc002ciq.2_Missense_Mutation_p.S19G|RHOT2_uc010bqy.2_5'Flank	NM_138769	NP_620124	Q8IXI1	MIRO2_HUMAN	ras homolog gene family, member T2	126	Miro 1.|Mitochondrial intermembrane (Potential).				apoptosis|cellular homeostasis|mitochondrion transport along microtubule|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|integral to mitochondrial outer membrane|plasma membrane	calcium ion binding|GTP binding|GTPase activity|protein binding			pancreas(1)	1		Hepatocellular(780;0.0218)																---	---	---	---
TMEM204	79652	broad.mit.edu	37	16	1591974	1591974	+	Silent	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1591974C>A	uc002cmc.2	+	3	731	c.333C>A	c.(331-333)ACC>ACA	p.T111T	IFT140_uc002clz.2_Intron|IFT140_uc002cmb.2_Intron|TMEM204_uc002cmd.2_Silent_p.T111T|TMEM204_uc010brr.1_Silent_p.T111T	NM_024600	NP_078876	Q9BSN7	TM204_HUMAN	transmembrane protein 204	111	Helical; (Potential).				response to stress	adherens junction|integral to membrane					0		Hepatocellular(780;0.219)																---	---	---	---
CRAMP1L	57585	broad.mit.edu	37	16	1705937	1705937	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1705937G>T	uc010uvh.1	+	9	1179	c.1179G>T	c.(1177-1179)AAG>AAT	p.K393N	CRAMP1L_uc002cmf.2_RNA	NM_020825	NP_065876	Q96RY5	CRML_HUMAN	Crm, cramped-like	393						nucleus	DNA binding				0																		---	---	---	---
GFER	2671	broad.mit.edu	37	16	2035989	2035989	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2035989A>C	uc002cob.2	+	3	648	c.578A>C	c.(577-579)GAG>GCG	p.E193A	GFER_uc002coc.2_Missense_Mutation_p.E118A	NM_005262	NP_005253	P55789	ALR_HUMAN	erv1-like growth factor	193	ERV/ALR sulfhydryl oxidase.				cell proliferation|spermatogenesis	extracellular region|mitochondrial intermembrane space	growth factor activity|thiol oxidase activity				0																		---	---	---	---
TSC2	7249	broad.mit.edu	37	16	2104453	2104453	+	Intron	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2104453C>A	uc002con.2	+						TSC2_uc010bsd.2_Intron|TSC2_uc002coo.2_Intron|TSC2_uc010uvv.1_Intron|TSC2_uc010uvw.1_Intron|TSC2_uc002cop.2_Intron	NM_000548	NP_000539			tuberous sclerosis 2 isoform 1						cell cycle arrest|endocytosis|heart development|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|negative regulation of cell size|negative regulation of phosphatidylinositol 3-kinase cascade|negative regulation of protein kinase B signaling cascade|negative regulation of TOR signaling cascade|negative regulation of Wnt receptor signaling pathway|nerve growth factor receptor signaling pathway|neural tube closure|phosphatidylinositol-mediated signaling|positive chemotaxis|protein import into nucleus|protein kinase B signaling cascade|regulation of endocytosis|regulation of insulin receptor signaling pathway|regulation of small GTPase mediated signal transduction	Golgi apparatus|nucleus|perinuclear region of cytoplasm|TSC1-TSC2 complex	GTPase activator activity|protein homodimerization activity			central_nervous_system(4)|lung(3)|ovary(2)|pancreas(1)	10		Hepatocellular(780;0.0202)						D|Mis|N|F|S			hamartoma|renal cell			Tuberous_Sclerosis				---	---	---	---
TSC2	7249	broad.mit.edu	37	16	2136747	2136747	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2136747G>A	uc002con.2	+	38	4970	c.4864G>A	c.(4864-4866)GCC>ACC	p.A1622T	TSC2_uc010bsd.2_Missense_Mutation_p.A1599T|TSC2_uc002coo.2_Missense_Mutation_p.A1555T|TSC2_uc010uvv.1_Missense_Mutation_p.A1519T|TSC2_uc010uvw.1_Missense_Mutation_p.A1507T|TSC2_uc002cop.2_Missense_Mutation_p.A1378T|TSC2_uc002coq.2_Missense_Mutation_p.A397T|TSC2_uc002cor.2_Missense_Mutation_p.A323T	NM_000548	NP_000539	P49815	TSC2_HUMAN	tuberous sclerosis 2 isoform 1	1622	Rap-GAP.				cell cycle arrest|endocytosis|heart development|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|negative regulation of cell size|negative regulation of phosphatidylinositol 3-kinase cascade|negative regulation of protein kinase B signaling cascade|negative regulation of TOR signaling cascade|negative regulation of Wnt receptor signaling pathway|nerve growth factor receptor signaling pathway|neural tube closure|phosphatidylinositol-mediated signaling|positive chemotaxis|protein import into nucleus|protein kinase B signaling cascade|regulation of endocytosis|regulation of insulin receptor signaling pathway|regulation of small GTPase mediated signal transduction	Golgi apparatus|nucleus|perinuclear region of cytoplasm|TSC1-TSC2 complex	GTPase activator activity|protein homodimerization activity			central_nervous_system(4)|lung(3)|ovary(2)|pancreas(1)	10		Hepatocellular(780;0.0202)						D|Mis|N|F|S			hamartoma|renal cell			Tuberous_Sclerosis				---	---	---	---
E4F1	1877	broad.mit.edu	37	16	2285135	2285135	+	Silent	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2285135C>A	uc002cpm.2	+	13	2037	c.1989C>A	c.(1987-1989)ACC>ACA	p.T663T	E4F1_uc010bsi.2_Missense_Mutation_p.P646H|E4F1_uc010bsj.2_Silent_p.T486T|DNASE1L2_uc002cpn.2_5'Flank|DNASE1L2_uc002cpo.2_5'Flank|DNASE1L2_uc002cpp.2_5'Flank|DNASE1L2_uc002cpq.2_5'Flank	NM_004424	NP_004415	Q66K89	E4F1_HUMAN	p120E4F	663					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																		---	---	---	---
SRRM2	23524	broad.mit.edu	37	16	2812958	2812958	+	Missense_Mutation	SNP	C	T	T	rs140913607	byFrequency	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2812958C>T	uc002crk.2	+	11	2978	c.2429C>T	c.(2428-2430)ACG>ATG	p.T810M	SRRM2_uc002crj.1_Missense_Mutation_p.T714M|SRRM2_uc002crl.1_Missense_Mutation_p.T810M|SRRM2_uc010bsu.1_Missense_Mutation_p.T714M	NM_016333	NP_057417	Q9UQ35	SRRM2_HUMAN	splicing coactivator subunit SRm300	810	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																		---	---	---	---
SRRM2	23524	broad.mit.edu	37	16	2813429	2813429	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2813429A>G	uc002crk.2	+	11	3449	c.2900A>G	c.(2899-2901)TAC>TGC	p.Y967C	SRRM2_uc002crj.1_Missense_Mutation_p.Y871C|SRRM2_uc002crl.1_Missense_Mutation_p.Y967C|SRRM2_uc010bsu.1_Missense_Mutation_p.Y871C	NM_016333	NP_057417	Q9UQ35	SRRM2_HUMAN	splicing coactivator subunit SRm300	967	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																		---	---	---	---
ZNF434	54925	broad.mit.edu	37	16	3433073	3433073	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3433073G>A	uc002cuz.2	-	6	2039	c.1237C>T	c.(1237-1239)CGC>TGC	p.R413C	ZNF434_uc002cux.3_Missense_Mutation_p.R624C|ZNF434_uc010uwx.1_Missense_Mutation_p.R336C|ZNF434_uc002cuy.3_Missense_Mutation_p.R336C	NM_017810	NP_060280	Q9NX65	ZN434_HUMAN	zinc finger protein 434	413	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2																		---	---	---	---
ANKS3	124401	broad.mit.edu	37	16	4764087	4764087	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4764087G>A	uc002cxj.1	-	7	969	c.674C>T	c.(673-675)TCG>TTG	p.S225L	ANKS3_uc002cxi.1_Missense_Mutation_p.S152L|ANKS3_uc002cxk.2_Missense_Mutation_p.S96L|ANKS3_uc002cxl.2_Missense_Mutation_p.S52L|ANKS3_uc010uxs.1_Missense_Mutation_p.S152L|ANKS3_uc002cxm.2_Missense_Mutation_p.S19L	NM_133450	NP_597707	Q6ZW76	ANKS3_HUMAN	ankyrin repeat and sterile alpha motif domain	225											0																		---	---	---	---
FAM86A	196483	broad.mit.edu	37	16	5140288	5140288	+	Missense_Mutation	SNP	C	A	A	rs144582297	byFrequency	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5140288C>A	uc002cyo.2	-	6	588	c.539G>T	c.(538-540)CGC>CTC	p.R180L	FAM86A_uc002cyp.2_Missense_Mutation_p.R146L	NM_201400	NP_958802	Q96G04	FA86A_HUMAN	hypothetical protein LOC196483 isoform 1	180											0																		---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	7645541	7645541	+	Intron	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7645541C>A	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)														---	---	---	---
C16orf68	79091	broad.mit.edu	37	16	8719642	8719642	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8719642C>T	uc002cyz.2	+	2	396	c.120C>T	c.(118-120)AGC>AGT	p.S40S	C16orf68_uc002cza.2_Silent_p.S40S	NM_024109	NP_077014	Q9BUU2	MET22_HUMAN	hypothetical protein LOC79091	40							methyltransferase activity				0																		---	---	---	---
PMM2	5373	broad.mit.edu	37	16	8895724	8895724	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8895724C>T	uc002czf.3	+	2	205	c.135C>T	c.(133-135)GGC>GGT	p.G45G	PMM2_uc010uyf.1_RNA|PMM2_uc010uyg.1_5'UTR|PMM2_uc010uyh.1_5'UTR|PMM2_uc010buj.2_RNA|PMM2_uc010uyi.1_5'UTR|PMM2_uc010uye.1_Silent_p.G45G	NM_000303	NP_000294	O15305	PMM2_HUMAN	phosphomannomutase 2	45					dolichol-linked oligosaccharide biosynthetic process|GDP-mannose biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	cytosol	phosphomannomutase activity			ovary(1)	1																		---	---	---	---
ZC3H7A	29066	broad.mit.edu	37	16	11855347	11855347	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11855347G>A	uc002dbk.2	-	18	2432	c.2234C>T	c.(2233-2235)GCG>GTG	p.A745V	ZC3H7A_uc002dbi.2_5'Flank|ZC3H7A_uc002dbj.2_RNA|ZC3H7A_uc002dbl.2_Missense_Mutation_p.A745V|ZC3H7A_uc002dbm.1_Missense_Mutation_p.A655V	NM_014153	NP_054872	Q8IWR0	Z3H7A_HUMAN	zinc finger CCCH-type containing 7A	745						nucleus	nucleic acid binding|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
ABCC6	368	broad.mit.edu	37	16	16251547	16251547	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16251547C>T	uc002den.3	-	27	3892	c.3855G>A	c.(3853-3855)GTG>GTA	p.V1285V	ABCC6_uc010bvo.2_RNA|ABCC6_uc002dem.2_5'Flank	NM_001171	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C, member 6	1285	Cytoplasmic (By similarity).|ABC transporter 2.				response to drug|visual perception	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			skin(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)														---	---	---	---
SMG1	23049	broad.mit.edu	37	16	18851223	18851223	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18851223G>A	uc002dfm.2	-	42	7105	c.6742C>T	c.(6742-6744)CGT>TGT	p.R2248C	SMG1_uc010bwb.2_Missense_Mutation_p.R2108C|SMG1_uc010bwa.2_Missense_Mutation_p.R979C|SMG1_uc002dfo.3_Missense_Mutation_p.R546C	NM_015092	NP_055907	Q96Q15	SMG1_HUMAN	PI-3-kinase-related kinase SMG-1	2248	PI3K/PI4K.				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																		---	---	---	---
DNAH3	55567	broad.mit.edu	37	16	20996759	20996759	+	Missense_Mutation	SNP	T	C	C	rs143224214		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20996759T>C	uc010vbe.1	-	48	7305	c.7305A>G	c.(7303-7305)ATA>ATG	p.I2435M	DNAH3_uc010vbd.1_5'Flank	NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	2435	ATP (Potential).|AAA 4 (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)														---	---	---	---
CDR2	1039	broad.mit.edu	37	16	22358879	22358879	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22358879G>A	uc002dkn.2	-	5	1080	c.772C>T	c.(772-774)CGA>TGA	p.R258*		NM_001802	NP_001793	Q01850	CDR2_HUMAN	cerebellar degeneration-related protein 2	258	Potential.					nucleus	protein binding			skin(1)	1				GBM - Glioblastoma multiforme(48;0.0188)														---	---	---	---
SLC5A11	115584	broad.mit.edu	37	16	24922690	24922690	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24922690C>A	uc002dmu.2	+	16	2096	c.1864C>A	c.(1864-1866)CTG>ATG	p.L622M	SLC5A11_uc002dms.2_Missense_Mutation_p.L558M|SLC5A11_uc010vcd.1_Missense_Mutation_p.L587M|SLC5A11_uc002dmt.2_Missense_Mutation_p.L466M|SLC5A11_uc010vce.1_Missense_Mutation_p.L552M|SLC5A11_uc010bxt.2_Missense_Mutation_p.L558M|SLC5A11_uc002dmv.2_Missense_Mutation_p.L245M	NM_052944	NP_443176	Q8WWX8	SC5AB_HUMAN	solute carrier family 5 (sodium/glucose	622	Cytoplasmic (Potential).				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)														---	---	---	---
XPO6	23214	broad.mit.edu	37	16	28112852	28112852	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28112852T>A	uc002dpa.1	-	23	3704	c.3203A>T	c.(3202-3204)GAG>GTG	p.E1068V	XPO6_uc002dpb.1_Missense_Mutation_p.E1054V|XPO6_uc010vcp.1_Missense_Mutation_p.E1067V	NM_015171	NP_055986	Q96QU8	XPO6_HUMAN	exportin 6	1068					protein export from nucleus		protein binding|protein transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
ITGAM	3684	broad.mit.edu	37	16	31342530	31342530	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31342530G>A	uc002ebq.2	+	29	3419	c.3321G>A	c.(3319-3321)CCG>CCA	p.P1107P	ITGAM_uc002ebr.2_Silent_p.P1108P|ITGAM_uc010can.2_Silent_p.P513P	NM_000632	NP_000623	P11215	ITAM_HUMAN	integrin alpha M isoform 2 precursor	1107	Helical; (Potential).				blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration	integrin complex	glycoprotein binding|receptor activity			kidney(1)	1																		---	---	---	---
ITGAD	3681	broad.mit.edu	37	16	31426188	31426188	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31426188T>C	uc002ebv.1	+	18	2208	c.2159T>C	c.(2158-2160)GTG>GCG	p.V720A	ITGAD_uc010cap.1_Missense_Mutation_p.V721A	NM_005353	NP_005344	Q13349	ITAD_HUMAN	integrin, alpha D precursor	720	Extracellular (Potential).				cell-cell adhesion|cell-matrix adhesion|immune response|integrin-mediated signaling pathway	integrin complex	receptor activity			skin(1)	1																		---	---	---	---
PHKB	5257	broad.mit.edu	37	16	47536999	47536999	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47536999A>G	uc002eev.3	+	4	455	c.403A>G	c.(403-405)AAG>GAG	p.K135E	PHKB_uc010vgi.1_Missense_Mutation_p.K128E|PHKB_uc002eeu.3_Missense_Mutation_p.K128E	NM_000293	NP_000284	Q93100	KPBB_HUMAN	phosphorylase kinase, beta isoform a	135					glucose metabolic process|glycogen catabolic process	cytosol|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity			ovary(1)|large_intestine(1)|breast(1)	3		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)																---	---	---	---
LONP2	83752	broad.mit.edu	37	16	48295348	48295348	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48295348G>A	uc002efi.1	+	5	826	c.737G>A	c.(736-738)CGC>CAC	p.R246H	LONP2_uc010vgm.1_RNA|LONP2_uc002efj.1_Missense_Mutation_p.R202H	NM_031490	NP_113678	Q86WA8	LONP2_HUMAN	peroxisomal LON protease-like	246					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																		---	---	---	---
ZNF423	23090	broad.mit.edu	37	16	49670094	49670094	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49670094C>T	uc002efs.2	-	5	3267	c.2969G>A	c.(2968-2970)TGT>TAT	p.C990Y	ZNF423_uc010vgn.1_Missense_Mutation_p.C873Y	NM_015069	NP_055884	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	990					cell differentiation|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(1)|lung(1)|kidney(1)|pancreas(1)	4		all_cancers(37;0.0155)																---	---	---	---
NKD1	85407	broad.mit.edu	37	16	50655551	50655551	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50655551G>A	uc002egg.1	+	5	522	c.298G>A	c.(298-300)GGA>AGA	p.G100R		NM_033119	NP_149110	Q969G9	NKD1_HUMAN	naked cuticle homolog 1	100					Wnt receptor signaling pathway	cytoplasm|plasma membrane	calcium ion binding|protein binding				0		all_cancers(37;0.229)		GBM - Glioblastoma multiforme(240;0.243)														---	---	---	---
NOD2	64127	broad.mit.edu	37	16	50745960	50745960	+	Missense_Mutation	SNP	G	A	A	rs104895483	byFrequency	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50745960G>A	uc002egm.1	+	4	2243	c.2138G>A	c.(2137-2139)CGC>CAC	p.R713H	NOD2_uc010cbk.1_Missense_Mutation_p.R686H|NOD2_uc002egl.1_Missense_Mutation_p.R491H|NOD2_uc010cbl.1_Missense_Mutation_p.R491H|NOD2_uc010cbm.1_Missense_Mutation_p.R491H|NOD2_uc010cbn.1_RNA|NOD2_uc010cbo.1_RNA|NOD2_uc010cbp.1_5'Flank|NOD2_uc010cbq.1_5'Flank|NOD2_uc010cbr.1_5'Flank	NM_022162	NP_071445	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain	713			R -> C (associated with Crohn disease).		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)																---	---	---	---
CHD9	80205	broad.mit.edu	37	16	53338134	53338134	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53338134A>G	uc002ehb.2	+	30	6380	c.6216A>G	c.(6214-6216)CTA>CTG	p.L2072L	CHD9_uc002egy.2_Silent_p.L2072L|CHD9_uc002ehc.2_Silent_p.L2072L|CHD9_uc002ehf.2_Silent_p.L1186L|CHD9_uc010cbw.2_Intron|CHD9_uc002ehg.1_Silent_p.L78L	NM_025134	NP_079410	Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	2072					cellular lipid metabolic process|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleoplasm	ATP binding|DNA binding|helicase activity|protein binding			lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1)	7		all_cancers(37;0.0212)																---	---	---	---
RBL2	5934	broad.mit.edu	37	16	53504679	53504679	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53504679C>T	uc002ehi.3	+	17	2666	c.2548C>T	c.(2548-2550)CGC>TGC	p.R850C	RBL2_uc002ehj.2_Missense_Mutation_p.R560C|RBL2_uc010vgw.1_Intron	NM_005611	NP_005602	Q08999	RBL2_HUMAN	retinoblastoma-like 2 (p130)	850	Domain B.|Pocket; binds E1A.				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																		---	---	---	---
GPR114	221188	broad.mit.edu	37	16	57608772	57608772	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57608772C>T	uc002elx.3	+	11	1339	c.1254C>T	c.(1252-1254)GGC>GGT	p.G418G	GPR114_uc010vhr.1_Missense_Mutation_p.A379V|GPR114_uc002ely.2_Silent_p.G418G	NM_153837	NP_722579	Q8IZF4	GP114_HUMAN	G protein-coupled receptor 114 precursor	418	Helical; Name=5; (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(1)	1																		---	---	---	---
KATNB1	10300	broad.mit.edu	37	16	57785591	57785591	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57785591C>T	uc002eml.1	+	7	845	c.471C>T	c.(469-471)CCC>CCT	p.P157P		NM_005886	NP_005877	Q9BVA0	KTNB1_HUMAN	katanin p80 subunit B 1	157	Interaction with centrosomes.|Interaction with dynein (By similarity).|WD 4.				cell division|mitosis|negative regulation of microtubule depolymerization|positive regulation of microtubule depolymerization|protein targeting	katanin complex|microtubule|spindle pole	microtubule binding|protein heterodimerization activity				0		all_neural(199;0.223)																---	---	---	---
CNGB1	1258	broad.mit.edu	37	16	57949172	57949172	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57949172C>T	uc002emt.2	-	23	2350	c.2285G>A	c.(2284-2286)CGC>CAC	p.R762H	CNGB1_uc010cdh.2_Missense_Mutation_p.R756H	NM_001297	NP_001288	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1 isoform	762	Extracellular (Potential).				sensory perception of smell	intracellular cyclic nucleotide activated cation channel complex	cAMP binding|intracellular cAMP activated cation channel activity			breast(3)|pancreas(1)	4																		---	---	---	---
PRSS54	221191	broad.mit.edu	37	16	58319861	58319861	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58319861C>A	uc002enf.2	-	5	897	c.502G>T	c.(502-504)GGA>TGA	p.G168*	PRSS54_uc002eng.2_Nonsense_Mutation_p.G168*|PRSS54_uc010vie.1_Nonsense_Mutation_p.G69*	NM_001080492	NP_001073961	Q6PEW0	PRS54_HUMAN	plasma kallikrein-like protein 4 precursor	168	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3																		---	---	---	---
CDH5	1003	broad.mit.edu	37	16	66424469	66424469	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66424469C>T	uc002eom.3	+	6	1101	c.945C>T	c.(943-945)AAC>AAT	p.N315N	CDH5_uc002eon.1_Silent_p.N315N	NM_001795	NP_001786	P33151	CADH5_HUMAN	cadherin 5, type 2 preproprotein	315	Cadherin 3.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion|regulation of establishment of cell polarity	integral to membrane|membrane fraction	beta-catenin binding|calcium ion binding|ion channel binding|receptor binding			ovary(2)|lung(2)|central_nervous_system(1)|skin(1)	6		Ovarian(137;0.0955)		OV - Ovarian serous cystadenocarcinoma(108;0.107)														---	---	---	---
CES3	23491	broad.mit.edu	37	16	67006362	67006362	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67006362T>C	uc002eqt.2	+	11	1468	c.1395T>C	c.(1393-1395)GCT>GCC	p.A465A	CES3_uc010cdz.2_Silent_p.A465A|CES3_uc010cea.2_RNA|CES3_uc010viw.1_Silent_p.A104A	NM_024922	NP_079198	Q6UWW8	EST3_HUMAN	carboxylesterase 3 precursor	465						endoplasmic reticulum lumen	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity			ovary(3)|central_nervous_system(2)	5		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0488)|Epithelial(162;0.127)														---	---	---	---
ELMO3	79767	broad.mit.edu	37	16	67235748	67235748	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67235748C>T	uc002esa.2	+	11	1224	c.1181C>T	c.(1180-1182)GCC>GTC	p.A394V	ELMO3_uc002esb.2_Missense_Mutation_p.A377V|ELMO3_uc002esc.2_Missense_Mutation_p.A228V	NM_024712	NP_078988	Q96BJ8	ELMO3_HUMAN	engulfment and cell motility 3	341	ELMO.				apoptosis|phagocytosis	cytoplasm|cytoskeleton	SH3 domain binding				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00067)|Epithelial(162;0.00442)|all cancers(182;0.0417)														---	---	---	---
PLEKHG4	25894	broad.mit.edu	37	16	67314404	67314404	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67314404C>A	uc002eso.3	+	1	2992	c.457C>A	c.(457-459)CTT>ATT	p.L153I	PLEKHG4_uc002esp.3_5'UTR|PLEKHG4_uc002esq.3_Missense_Mutation_p.L153I|PLEKHG4_uc002esr.1_Intron|PLEKHG4_uc010cef.2_Missense_Mutation_p.L153I|PLEKHG4_uc002ess.3_Missense_Mutation_p.L153I|PLEKHG4_uc010ceg.2_Intron	NM_015432	NP_056247	Q58EX7	PKHG4_HUMAN	pleckstrin homology domain containing, family G	153					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			skin(1)|pancreas(1)	2				OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)|Kidney(780;0.119)														---	---	---	---
EDC4	23644	broad.mit.edu	37	16	67914579	67914579	+	Silent	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67914579C>A	uc002eur.2	+	18	2383	c.2217C>A	c.(2215-2217)GCC>GCA	p.A739A	EDC4_uc010cer.2_Silent_p.A358A|EDC4_uc002eus.2_Silent_p.A469A|EDC4_uc002eut.1_5'Flank	NM_014329	NP_055144	Q6P2E9	EDC4_HUMAN	autoantigen RCD8	739					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	cytoplasmic mRNA processing body|cytosol|nucleus	protein binding			ovary(2)|central_nervous_system(2)	4		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)														---	---	---	---
EDC4	23644	broad.mit.edu	37	16	67916698	67916698	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67916698C>T	uc002eur.2	+	26	3725	c.3559C>T	c.(3559-3561)CAG>TAG	p.Q1187*	EDC4_uc010cer.2_Nonsense_Mutation_p.Q806*|EDC4_uc002eus.2_Nonsense_Mutation_p.Q917*|EDC4_uc002eut.1_Nonsense_Mutation_p.Q106*|NRN1L_uc002euu.2_5'Flank	NM_014329	NP_055144	Q6P2E9	EDC4_HUMAN	autoantigen RCD8	1187					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	cytoplasmic mRNA processing body|cytosol|nucleus	protein binding			ovary(2)|central_nervous_system(2)	4		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)												OREG0023890	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TMCO7	79613	broad.mit.edu	37	16	68877527	68877527	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68877527G>A	uc002ewi.3	+	1	19	c.7G>A	c.(7-9)GCC>ACC	p.A3T	TMCO7_uc002ewh.2_Missense_Mutation_p.A3T	NM_024562	NP_078838	Q9C0B7	TMCO7_HUMAN	transmembrane and coiled-coil domains 7	3						integral to membrane	binding				0		Ovarian(137;0.0568)		OV - Ovarian serous cystadenocarcinoma(108;0.0446)|Epithelial(162;0.198)														---	---	---	---
WWP2	11060	broad.mit.edu	37	16	69833085	69833085	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69833085C>T	uc002exu.1	+	5	316	c.227C>T	c.(226-228)ACG>ATG	p.T76M	WWP2_uc002ext.2_Missense_Mutation_p.T76M|WWP2_uc002exv.1_Missense_Mutation_p.T76M	NM_007014	NP_008945	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase	76	C2.				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																OREG0023909	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
WWP2	11060	broad.mit.edu	37	16	69965432	69965432	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69965432C>T	uc002exu.1	+	16	1631	c.1542C>T	c.(1540-1542)CAC>CAT	p.H514H	WWP2_uc002exv.1_Silent_p.H514H|WWP2_uc010vlm.1_Silent_p.H398H|WWP2_uc010vln.1_Silent_p.H132H|WWP2_uc002exw.1_Silent_p.H75H|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	514					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																		---	---	---	---
ZFHX3	463	broad.mit.edu	37	16	72829201	72829201	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72829201G>A	uc002fck.2	-	9	8053	c.7380C>T	c.(7378-7380)CCC>CCT	p.P2460P	ZFHX3_uc002fcl.2_Silent_p.P1546P	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A	2460					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)																---	---	---	---
PSMD7	5713	broad.mit.edu	37	16	74334047	74334047	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74334047G>A	uc002fcq.2	+	2	241	c.109G>A	c.(109-111)GGT>AGT	p.G37S	PSMD7_uc010vmr.1_5'UTR	NM_002811	NP_002802	P51665	PSD7_HUMAN	proteasome 26S non-ATPase subunit 7	37	MPN.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome regulatory particle	protein binding				0																		---	---	---	---
MLKL	197259	broad.mit.edu	37	16	74709625	74709625	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74709625A>G	uc002fdb.2	-	8	1517	c.1076T>C	c.(1075-1077)ATG>ACG	p.M359T	MLKL_uc002fdc.2_Intron	NM_152649	NP_689862	Q8NB16	MLKL_HUMAN	mixed lineage kinase domain-like isoform 1	359	Protein kinase.						ATP binding|protein binding|protein kinase activity			stomach(2)	2																		---	---	---	---
LDHD	197257	broad.mit.edu	37	16	75148095	75148095	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75148095A>G	uc002fdm.2	-	6	714	c.667T>C	c.(667-669)TGG>CGG	p.W223R	LDHD_uc002fdn.2_Intron	NM_153486	NP_705690	Q86WU2	LDHD_HUMAN	D-lactate dehydrogenase isoform 1 precursor	223	FAD-binding PCMH-type.						D-lactate dehydrogenase (cytochrome) activity|flavin adenine dinucleotide binding|protein binding				0																		---	---	---	---
KARS	3735	broad.mit.edu	37	16	75662478	75662478	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75662478T>C	uc002feq.2	-	13	1732	c.1684A>G	c.(1684-1686)AAC>GAC	p.N562D	KARS_uc002fer.2_Missense_Mutation_p.N590D|KARS_uc002fes.2_Missense_Mutation_p.N406D	NM_005548	NP_005539	Q15046	SYK_HUMAN	lysyl-tRNA synthetase isoform 2	562					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)													---	---	---	---
VAT1L	57687	broad.mit.edu	37	16	77910345	77910345	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77910345A>C	uc002ffg.1	+	5	898	c.801A>C	c.(799-801)AAA>AAC	p.K267N		NM_020927	NP_065978	Q9HCJ6	VAT1L_HUMAN	vesicle amine transport protein 1 homolog (T.	267							oxidoreductase activity|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
CDYL2	124359	broad.mit.edu	37	16	80718849	80718849	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80718849A>C	uc002ffs.2	-	2	307	c.202T>G	c.(202-204)TCA>GCA	p.S68A		NM_152342	NP_689555	Q8N8U2	CDYL2_HUMAN	chromodomain protein, Y-like 2	68						nucleus	catalytic activity|protein binding			central_nervous_system(1)	1																		---	---	---	---
BCMO1	53630	broad.mit.edu	37	16	81320960	81320960	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81320960C>T	uc002fgn.1	+	10	1581	c.1363C>T	c.(1363-1365)CCA>TCA	p.P455S	BCMO1_uc010vnp.1_Missense_Mutation_p.P386S	NM_017429	NP_059125	Q9HAY6	BCDO1_HUMAN	beta-carotene 15,15'-monooxygenase	455					retinoid metabolic process|steroid metabolic process	cytosol	beta-carotene 15,15'-monooxygenase activity|metal ion binding|monooxygenase activity				0																		---	---	---	---
HSD17B2	3294	broad.mit.edu	37	16	82131764	82131764	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82131764G>A	uc002fgv.2	+	5	1059	c.887G>A	c.(886-888)GGC>GAC	p.G296D		NM_002153	NP_002144	P37059	DHB2_HUMAN	hydroxysteroid (17-beta) dehydrogenase 2	296					response to retinoic acid|steroid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity|binding|estradiol 17-beta-dehydrogenase activity|testosterone 17-beta-dehydrogenase (NAD+) activity			ovary(1)|central_nervous_system(1)	2					NADH(DB00157)													---	---	---	---
CDH13	1012	broad.mit.edu	37	16	83251067	83251067	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83251067C>T	uc002fgx.2	+	5	721	c.601C>T	c.(601-603)CGG>TGG	p.R201W	CDH13_uc010vns.1_Missense_Mutation_p.R248W|CDH13_uc010vnt.1_Translation_Start_Site|CDH13_uc010vnu.1_Missense_Mutation_p.R162W	NM_001257	NP_001248	P55290	CAD13_HUMAN	cadherin 13 preproprotein	201	Cadherin 1.				adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)														---	---	---	---
ATP2C2	9914	broad.mit.edu	37	16	84442023	84442023	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84442023C>A	uc002fhx.2	+	4	429	c.340C>A	c.(340-342)CTG>ATG	p.L114M	ATP2C2_uc010chj.2_Missense_Mutation_p.L114M|ATP2C2_uc002fhy.2_Missense_Mutation_p.L131M|ATP2C2_uc002fhz.2_Translation_Start_Site	NM_014861	NP_055676	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	114	Poly-Leu.|Helical; Name=1; (Potential).				ATP biosynthetic process	Golgi membrane|integral to membrane	ATP binding|calcium-transporting ATPase activity|metal ion binding|protein binding			breast(1)|central_nervous_system(1)	2																		---	---	---	---
JPH3	57338	broad.mit.edu	37	16	87678632	87678632	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87678632C>T	uc002fkd.2	+	2	1405	c.1151C>T	c.(1150-1152)GCG>GTG	p.A384V	JPH3_uc010vou.1_RNA	NM_020655	NP_065706	Q8WXH2	JPH3_HUMAN	junctophilin 3	384	Ala-rich.|Cytoplasmic (Potential).				calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane|plasma membrane	protein binding			ovary(1)|pancreas(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0287)														---	---	---	---
ANKRD11	29123	broad.mit.edu	37	16	89347911	89347911	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89347911A>G	uc002fmx.1	-	9	5500	c.5039T>C	c.(5038-5040)CTG>CCG	p.L1680P	ANKRD11_uc002fmy.1_Missense_Mutation_p.L1680P|ANKRD11_uc002fnc.1_Missense_Mutation_p.L1680P|ANKRD11_uc002fna.1_5'Flank|ANKRD11_uc002fnb.1_Missense_Mutation_p.L1637P	NM_013275	NP_037407	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	1680						nucleus				ovary(4)|large_intestine(1)|central_nervous_system(1)	6		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)														---	---	---	---
TUBB3	10381	broad.mit.edu	37	16	90001715	90001715	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90001715G>A	uc002fph.1	+	4	921	c.856G>A	c.(856-858)GTG>ATG	p.V286M	TUBB3_uc002fpf.2_Missense_Mutation_p.V633M|TUBB3_uc010ciz.1_Missense_Mutation_p.V214M|TUBB3_uc002fpg.1_Missense_Mutation_p.V140M|TUBB3_uc002fpi.1_Missense_Mutation_p.V214M|TUBB3_uc002fpj.1_Missense_Mutation_p.V214M|TUBB3_uc010cjb.1_Missense_Mutation_p.V140M|TUBB3_uc002fpk.1_Missense_Mutation_p.V140M	NM_006086	NP_006077	Q13509	TBB3_HUMAN	tubulin, beta, 4	286					'de novo' posttranslational protein folding|axon guidance|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity			ovary(2)|pancreas(1)	3		all_cancers(9;1.69e-11)|Lung NSC(15;8.94e-06)|all_lung(18;1.39e-05)|all_neural(9;0.00581)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0273)														---	---	---	---
ABR	29	broad.mit.edu	37	17	994966	994966	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:994966A>G	uc002fsd.2	-	4	580	c.470T>C	c.(469-471)CTG>CCG	p.L157P	ABR_uc002fse.2_Missense_Mutation_p.L111P|ABR_uc002fsg.2_Missense_Mutation_p.L120P|ABR_uc002fsh.1_Missense_Mutation_p.L41P|ABR_uc010cjq.1_Missense_Mutation_p.L169P	NM_021962	NP_068781	Q12979	ABR_HUMAN	active breakpoint cluster region-related	157	DH.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)														---	---	---	---
SMG6	23293	broad.mit.edu	37	17	2202478	2202478	+	Silent	SNP	C	T	T	rs147802850	byFrequency	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2202478C>T	uc002fub.1	-	2	1624	c.1569G>A	c.(1567-1569)ACG>ACA	p.T523T	SMG6_uc002fud.1_Silent_p.T492T	NM_017575	NP_060045	Q86US8	EST1A_HUMAN	Smg-6 homolog, nonsense mediated mRNA decay	523					mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation|telomere maintenance	chromosome, telomeric region|cytosol|nucleolus|telomerase holoenzyme complex	endoribonuclease activity|metal ion binding|protein binding|telomeric DNA binding			central_nervous_system(2)|lung(1)|kidney(1)	4																		---	---	---	---
SMG6	23293	broad.mit.edu	37	17	2202891	2202891	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2202891C>A	uc002fub.1	-	2	1211	c.1156G>T	c.(1156-1158)GGC>TGC	p.G386C	SMG6_uc002fud.1_Missense_Mutation_p.G355C	NM_017575	NP_060045	Q86US8	EST1A_HUMAN	Smg-6 homolog, nonsense mediated mRNA decay	386	Interaction with telomeric DNA.				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																		---	---	---	---
TSR1	55720	broad.mit.edu	37	17	2238160	2238160	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2238160G>T	uc002fuj.2	-	5	1544	c.587C>A	c.(586-588)CCA>CAA	p.P196Q	SGSM2_uc002fum.3_5'Flank|SGSM2_uc010vqw.1_5'Flank|SGSM2_uc002fun.3_5'Flank	NM_018128	NP_060598	Q2NL82	TSR1_HUMAN	TSR1, 20S rRNA accumulation	196					ribosome assembly	nucleolus	protein binding			ovary(1)	1																		---	---	---	---
KIAA0664	23277	broad.mit.edu	37	17	2595998	2595998	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2595998C>T	uc002fuy.1	-						KIAA0664_uc002fux.1_Intron|KIAA0664_uc010ckc.1_Intron	NM_015229	NP_056044			hypothetical protein LOC23277								binding			breast(2)	2																		---	---	---	---
KIAA0664	23277	broad.mit.edu	37	17	2598782	2598782	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2598782G>A	uc002fuy.1	-	14	2399	c.2313C>T	c.(2311-2313)GAC>GAT	p.D771D	KIAA0664_uc002fux.1_Silent_p.D704D|KIAA0664_uc010ckc.1_5'Flank	NM_015229	NP_056044	O75153	K0664_HUMAN	hypothetical protein LOC23277	771							binding			breast(2)	2																		---	---	---	---
SMTNL2	342527	broad.mit.edu	37	17	4495754	4495754	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4495754C>T	uc002fyf.1	+						SMTNL2_uc002fye.2_Intron	NM_001114974	NP_001108446			smoothelin-like 2 isoform 1												0				READ - Rectum adenocarcinoma(115;0.0325)														---	---	---	---
ARRB2	409	broad.mit.edu	37	17	4621209	4621209	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4621209A>G	uc002fyj.2	+	8	740	c.512A>G	c.(511-513)AAG>AGG	p.K171R	ARRB2_uc002fyk.2_Missense_Mutation_p.K156R|ARRB2_uc002fyl.2_Missense_Mutation_p.K171R|ARRB2_uc010vsg.1_Missense_Mutation_p.K192R|ARRB2_uc002fym.2_Missense_Mutation_p.K156R|ARRB2_uc002fyn.2_5'UTR|ARRB2_uc010ckq.2_5'UTR|ARRB2_uc002fyo.2_5'UTR	NM_004313	NP_004304	P32121	ARRB2_HUMAN	arrestin, beta 2 isoform 1	171					cell chemotaxis|desensitization of G-protein coupled receptor protein signaling pathway by arrestin|G-protein coupled receptor internalization|negative regulation of natural killer cell mediated cytotoxicity|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein ubiquitination|platelet activation|positive regulation of ERK1 and ERK2 cascade|proteasomal ubiquitin-dependent protein catabolic process|protein transport|protein ubiquitination|transcription from RNA polymerase II promoter|transforming growth factor beta receptor signaling pathway	coated pit|cytoplasmic membrane-bounded vesicle|cytosol|nucleus|plasma membrane	angiotensin receptor binding|ubiquitin protein ligase binding				0																		---	---	---	---
TM4SF5	9032	broad.mit.edu	37	17	4675310	4675310	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4675310T>C	uc002fyw.1	+	1	124	c.93T>C	c.(91-93)CCT>CCC	p.P31P		NM_003963	NP_003954	O14894	T4S5_HUMAN	transmembrane 4 superfamily member 5	31	Extracellular (Potential).					integral to plasma membrane				ovary(1)	1																		---	---	---	---
NLRP1	22861	broad.mit.edu	37	17	5433956	5433956	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5433956G>A	uc002gci.2	-	12	3920	c.3365C>T	c.(3364-3366)GCG>GTG	p.A1122V	NLRP1_uc002gcg.1_Missense_Mutation_p.A1126V|NLRP1_uc002gck.2_Missense_Mutation_p.A1122V|NLRP1_uc002gcj.2_Missense_Mutation_p.A1092V|NLRP1_uc002gcl.2_Missense_Mutation_p.A1092V|NLRP1_uc002gch.3_Missense_Mutation_p.A1122V|NLRP1_uc010clh.2_Missense_Mutation_p.A1122V	NM_033004	NP_127497	Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1 isoform 1	1122					defense response to bacterium|induction of apoptosis|neuron apoptosis|positive regulation of interleukin-1 beta secretion|response to muramyl dipeptide	cytoplasm|NALP1 inflammasome complex|nucleus	ATP binding|caspase activator activity|enzyme binding|protein domain specific binding			lung(4)|breast(2)|ovary(1)|central_nervous_system(1)|skin(1)	9		Colorectal(1115;3.48e-05)																---	---	---	---
SLC13A5	284111	broad.mit.edu	37	17	6610090	6610090	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6610090A>G	uc002gdj.2	-	3	327	c.239T>C	c.(238-240)GTC>GCC	p.V80A	SLC13A5_uc010vtf.1_Missense_Mutation_p.V80A|SLC13A5_uc010clq.2_Missense_Mutation_p.V37A|SLC13A5_uc002gdk.2_Missense_Mutation_p.V80A|SLC13A5_uc002gdl.1_5'Flank	NM_177550	NP_808218	Q86YT5	S13A5_HUMAN	solute carrier family 13, member 5 isoform a	80	Helical; (Potential).					integral to membrane	citrate transmembrane transporter activity				0																		---	---	---	---
BCL6B	255877	broad.mit.edu	37	17	6930285	6930285	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6930285C>T	uc002geg.2	+	8	1259	c.1202C>T	c.(1201-1203)GCG>GTG	p.A401V	BCL6B_uc010clt.1_Missense_Mutation_p.A402V	NM_181844	NP_862827	Q8N143	BCL6B_HUMAN	B-cell CLL/lymphoma 6, member B (zinc finger	401	C2H2-type 3.					nucleus	zinc ion binding			skin(1)	1																		---	---	---	---
DLG4	1742	broad.mit.edu	37	17	7096400	7096400	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7096400C>T	uc002get.3	-	19	3060	c.1859G>A	c.(1858-1860)GGC>GAC	p.G620D	DLG4_uc010vtm.1_RNA|DLG4_uc010vtn.1_Missense_Mutation_p.G517D|DLG4_uc010cly.2_Missense_Mutation_p.G574D|DLG4_uc010vto.1_Missense_Mutation_p.G617D	NM_001365	NP_001356	P78352	DLG4_HUMAN	post-synaptic density protein 95 isoform 1	577	Guanylate kinase-like.				axon guidance|learning|protein complex assembly|protein localization to synapse|signal transduction|synaptic transmission	cell junction|cortical cytoskeleton|endocytic vesicle membrane|neuron spine|postsynaptic density|postsynaptic membrane|synaptosome	protein binding|protein C-terminus binding			ovary(1)|breast(1)	2																		---	---	---	---
EIF5A	1984	broad.mit.edu	37	17	7214696	7214696	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7214696T>C	uc010vtv.1	+	4	535	c.298T>C	c.(298-300)TCA>CCA	p.S100P	EIF5A_uc002gfr.2_Missense_Mutation_p.S130P|EIF5A_uc002gft.2_Missense_Mutation_p.S100P|EIF5A_uc002gfu.2_Missense_Mutation_p.S100P	NM_001970	NP_001961	P63241	IF5A1_HUMAN	eukaryotic translation initiation factor 5A	100					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																		---	---	---	---
C17orf74	201243	broad.mit.edu	37	17	7330037	7330037	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7330037A>G	uc002ggw.2	+	3	800	c.727A>G	c.(727-729)ATG>GTG	p.M243V	FGF11_uc010vtw.1_Intron	NM_175734	NP_783861	Q0P670	CQ074_HUMAN	hypothetical protein LOC201243	243						integral to membrane					0		Prostate(122;0.157)																---	---	---	---
POLR2A	5430	broad.mit.edu	37	17	7412287	7412287	+	Missense_Mutation	SNP	A	G	G	rs111953899		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7412287A>G	uc002ghf.3	+	21	3724	c.3490A>G	c.(3490-3492)ACA>GCA	p.T1164A		NM_000937	NP_000928	P24928	RPB1_HUMAN	DNA-directed RNA polymerase II A	1164					mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|RNA-directed RNA polymerase activity|ubiquitin protein ligase binding			pancreas(1)	1		Prostate(122;0.173)																---	---	---	---
CD68	968	broad.mit.edu	37	17	7483133	7483133	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7483133G>A	uc002ghv.2	+	2	246	c.55G>A	c.(55-57)GGG>AGG	p.G19R	CD68_uc002ghu.2_Intron	NM_001251	NP_001242	P34810	CD68_HUMAN	CD68 antigen isoform A	19						endosome membrane|integral to membrane|lysosomal membrane|membrane fraction|plasma membrane					0																		---	---	---	---
TP53	7157	broad.mit.edu	37	17	7576877	7576877	+	Silent	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7576877C>A	uc002gim.2	-	9	1163	c.969G>T	c.(967-969)CTG>CTT	p.L323L	TP53_uc002gig.1_Intron|TP53_uc002gih.2_Silent_p.L323L|TP53_uc010cne.1_RNA|TP53_uc010cnf.1_Silent_p.L191L|TP53_uc010cng.1_Silent_p.L191L|TP53_uc002gii.1_Silent_p.L191L|TP53_uc010cnh.1_Silent_p.L323L|TP53_uc010cni.1_Silent_p.L323L|TP53_uc002gij.2_Silent_p.L323L	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	323	Interaction with HIPK1 (By similarity).|Interaction with CARM1.|Interaction with HIPK2.		L -> P (in a sporadic cancer; somatic mutation).|L -> R (in a sporadic cancer; somatic mutation).|L -> M (in a sporadic cancer; somatic mutation).|L -> G (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|L -> V (in a sporadic cancer; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.0?(7)|p.L323V(1)|p.P318fs*21(1)|p.?(1)|p.L323P(1)|p.L323G(1)|p.L323fs*22(1)|p.L323M(1)|p.L323R(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)			111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			---	---	---	---
WRAP53	55135	broad.mit.edu	37	17	7592608	7592608	+	Silent	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7592608C>A	uc010vuh.1	+	3	653	c.498C>A	c.(496-498)ACC>ACA	p.T166T	WRAP53_uc010vui.1_Silent_p.T166T|WRAP53_uc002gip.2_Silent_p.T166T|WRAP53_uc002gir.2_Silent_p.T166T|WRAP53_uc002giq.2_RNA|WRAP53_uc010cnl.2_Intron|TP53_uc010cnh.1_5'Flank|TP53_uc010cni.1_5'Flank|TP53_uc002gim.2_5'Flank|TP53_uc002gij.2_5'Flank|TP53_uc002gin.2_5'Flank|TP53_uc002gio.2_5'Flank|TP53_uc010vug.1_5'Flank|TP53_uc010cnk.1_5'Flank	NM_001143990	NP_001137462	Q9BUR4	WAP53_HUMAN	WD repeat domain 79 isoform 2	166					positive regulation of telomerase activity|telomere formation via telomerase	Cajal body|cytoplasm|telomerase holoenzyme complex	protein binding|RNA binding				0																		---	---	---	---
DNAH2	146754	broad.mit.edu	37	17	7646306	7646306	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7646306T>C	uc002giu.1	+	11	1764	c.1750T>C	c.(1750-1752)TAT>CAT	p.Y584H	DNAH2_uc002git.2_Missense_Mutation_p.Y666H|DNAH2_uc010vuk.1_Missense_Mutation_p.Y584H	NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3	584	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(6)|central_nervous_system(1)	13		all_cancers(10;4.66e-07)|Prostate(122;0.081)																---	---	---	---
KDM6B	23135	broad.mit.edu	37	17	7750709	7750709	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7750709G>C	uc002giw.1	+	10	1572	c.1196G>C	c.(1195-1197)AGC>ACC	p.S399T	KDM6B_uc002gix.2_5'Flank	NM_001080424	NP_001073893	O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	399	Pro-rich.				inflammatory response	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			central_nervous_system(1)|pancreas(1)	2																		---	---	---	---
KDM6B	23135	broad.mit.edu	37	17	7754822	7754822	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7754822A>G	uc002giw.1	+	16	4347	c.3971A>G	c.(3970-3972)CAC>CGC	p.H1324R	KDM6B_uc002gix.2_Missense_Mutation_p.H626R	NM_001080424	NP_001073893	O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	1324					inflammatory response	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			central_nervous_system(1)|pancreas(1)	2																		---	---	---	---
CHD3	1107	broad.mit.edu	37	17	7809874	7809874	+	Silent	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7809874C>A	uc002gje.2	+	29	4512	c.4362C>A	c.(4360-4362)GCC>GCA	p.A1454A	CHD3_uc002gjd.2_Silent_p.A1513A|CHD3_uc002gjf.2_Silent_p.A1454A|CHD3_uc002gjh.2_Silent_p.A30A|CHD3_uc002gjj.2_5'Flank	NM_001005273	NP_001005273	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	1454					chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|zinc ion binding			breast(1)	1		Prostate(122;0.202)																---	---	---	---
MYH13	8735	broad.mit.edu	37	17	10235439	10235439	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10235439G>A	uc002gmk.1	-	20	2365	c.2275C>T	c.(2275-2277)CAG>TAG	p.Q759*		NM_003802	NP_003793	Q9UKX3	MYH13_HUMAN	myosin, heavy polypeptide 13, skeletal muscle	759	Myosin head-like.				muscle contraction	muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|skin(2)	6																		---	---	---	---
MYH8	4626	broad.mit.edu	37	17	10302877	10302877	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10302877C>T	uc002gmm.2	-	28	3940	c.3845G>A	c.(3844-3846)CGC>CAC	p.R1282H	uc002gml.1_Intron	NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,	1282	Potential.				muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			skin(6)|ovary(3)|breast(2)	11														Trismus-Pseudocamptodactyly_Syndrome_with_Cardiac_Myxoma_and_Freckling				---	---	---	---
MYH2	4620	broad.mit.edu	37	17	10424716	10424716	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10424716G>A	uc010coi.2	-	40	5835	c.5707C>T	c.(5707-5709)CGC>TGC	p.R1903C	uc002gml.1_Intron|MYH1_uc002gmo.2_5'Flank|MYH2_uc002gmp.3_Missense_Mutation_p.R1903C|MYH2_uc010coj.2_Missense_Mutation_p.R670C	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	1903	Potential.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1)	14																		---	---	---	---
MYH3	4621	broad.mit.edu	37	17	10551944	10551944	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10551944A>G	uc002gmq.1	-	7	742	c.665T>C	c.(664-666)ATC>ACC	p.I222T		NM_002470	NP_002461	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle,	222	Myosin head-like.				muscle filament sliding|muscle organ development	cytosol|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|central_nervous_system(2)|pancreas(1)	7																		---	---	---	---
SREBF1	6720	broad.mit.edu	37	17	17719525	17719525	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17719525A>G	uc002gru.1	-	11	2404	c.2210T>C	c.(2209-2211)CTG>CCG	p.L737P	SREBF1_uc002grp.1_Missense_Mutation_p.L356P|SREBF1_uc002grq.1_Missense_Mutation_p.L256P|SREBF1_uc002grr.1_Missense_Mutation_p.L483P|SREBF1_uc002grs.1_Missense_Mutation_p.L713P|SREBF1_uc002grt.1_Missense_Mutation_p.L767P|MIR33B_hsa-mir-33b|MI0003646_5'Flank	NM_004176	NP_004167	P36956	SRBP1_HUMAN	sterol regulatory element binding transcription	737	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																		---	---	---	---
SLC5A10	125206	broad.mit.edu	37	17	18862493	18862493	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18862493A>G	uc002guu.1	+	3	270	c.229A>G	c.(229-231)ATT>GTT	p.I77V	SLC5A10_uc002gur.1_Missense_Mutation_p.I21V|SLC5A10_uc002gut.1_Missense_Mutation_p.I77V|SLC5A10_uc002guv.1_Missense_Mutation_p.I77V|SLC5A10_uc010vyl.1_Missense_Mutation_p.I77V	NM_001042450	NP_001035915	A0PJK1	SC5AA_HUMAN	solute carrier family 5 (sodium/glucose	77	Helical; (Potential).				sodium ion transport|transmembrane transport	integral to membrane	transporter activity			ovary(1)	1																		---	---	---	---
SLC5A10	125206	broad.mit.edu	37	17	18923686	18923686	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18923686G>A	uc002guu.1	+	15	1774	c.1733G>A	c.(1732-1734)GGC>GAC	p.G578D	SLC5A10_uc002gur.1_Missense_Mutation_p.G548D|SLC5A10_uc002gut.1_Missense_Mutation_p.G594D|SLC5A10_uc002guv.1_Missense_Mutation_p.G551D|SLC5A10_uc010vyl.1_Missense_Mutation_p.G542D	NM_001042450	NP_001035915	A0PJK1	SC5AA_HUMAN	solute carrier family 5 (sodium/glucose	578	Helical; (Potential).				sodium ion transport|transmembrane transport	integral to membrane	transporter activity			ovary(1)	1																		---	---	---	---
MAPK7	5598	broad.mit.edu	37	17	19284784	19284784	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19284784G>A	uc002gvn.2	+	4	1648	c.1262G>A	c.(1261-1263)AGT>AAT	p.S421N	MAPK7_uc002gvo.2_Missense_Mutation_p.S282N|MAPK7_uc002gvq.2_Missense_Mutation_p.S421N|MAPK7_uc002gvp.2_Missense_Mutation_p.S421N	NM_139033	NP_620602	Q13164	MK07_HUMAN	mitogen-activated protein kinase 7 isoform 1	421	May not be required for kinase activity; required to stimulate MEF2C activity (By similarity).|Pro-rich.				cell cycle|cell differentiation|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase activity|protein binding			central_nervous_system(4)|lung(3)|stomach(1)|skin(1)	9	all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206)																	---	---	---	---
AKAP10	11216	broad.mit.edu	37	17	19823371	19823371	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19823371T>C	uc002gwo.2	-	12	1949	c.1812A>G	c.(1810-1812)GAA>GAG	p.E604E	AKAP10_uc002gwp.1_Silent_p.E604E|AKAP10_uc010cqw.1_Silent_p.E546E	NM_007202	NP_009133	O43572	AKA10_HUMAN	A-kinase anchor protein 10 precursor	604					blood coagulation|protein localization	cytosol|mitochondrion|plasma membrane	signal transducer activity			skin(1)	1	all_cancers(12;2.08e-05)|all_epithelial(12;0.00158)|Breast(13;0.165)																	---	---	---	---
WSB1	26118	broad.mit.edu	37	17	25638603	25638603	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25638603G>A	uc002gzd.1	+	8	1383	c.1067G>A	c.(1066-1068)TGC>TAC	p.C356Y	WSB1_uc002gze.1_Missense_Mutation_p.C210Y|WSB1_uc002gzf.1_RNA	NM_015626	NP_056441	Q9Y6I7	WSB1_HUMAN	WD repeat and SOCS box-containing 1 isoform 1	356					intracellular signal transduction	intracellular	protein binding				0	all_cancers(1;2e-13)|all_epithelial(1;4.8e-15)|Lung NSC(42;0.00152)		BRCA - Breast invasive adenocarcinoma(3;0.0152)	UCEC - Uterine corpus endometrioid carcinoma (53;0.154)														---	---	---	---
MYO18A	399687	broad.mit.edu	37	17	27438782	27438782	+	Missense_Mutation	SNP	G	T	T	rs144602898	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27438782G>T	uc002hdt.1	-	16	2856	c.2698C>A	c.(2698-2700)CGC>AGC	p.R900S	MYO18A_uc010wbc.1_Missense_Mutation_p.R442S|MYO18A_uc002hds.2_Missense_Mutation_p.R442S|MYO18A_uc010csa.1_Missense_Mutation_p.R900S|MYO18A_uc002hdu.1_Missense_Mutation_p.R900S|MYO18A_uc010wbd.1_Missense_Mutation_p.R569S	NM_078471	NP_510880	Q92614	MY18A_HUMAN	myosin 18A isoform a	900	Myosin head-like.				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)													OREG0024287	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ANKRD13B	124930	broad.mit.edu	37	17	27934865	27934865	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27934865G>A	uc002hei.2	+	2	333	c.220G>A	c.(220-222)GTG>ATG	p.V74M	ANKRD13B_uc002heh.2_Translation_Start_Site|ANKRD13B_uc002hej.2_RNA	NM_152345	NP_689558	Q86YJ7	AN13B_HUMAN	ankyrin repeat domain 13B	74	ANK 1.										0																		---	---	---	---
SLC6A4	6532	broad.mit.edu	37	17	28536227	28536227	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28536227A>G	uc002hey.3	-	12	2027	c.1483T>C	c.(1483-1485)TAT>CAT	p.Y495H	SLC6A4_uc010csg.2_Intron	NM_001045	NP_001036	P31645	SC6A4_HUMAN	solute carrier family 6 member 4	495					response to toxin|serotonin uptake|thalamus development	cytosol|endomembrane system|endosome membrane|membrane raft	actin filament binding|Rab GTPase binding|serotonin transmembrane transporter activity|serotonin:sodium symporter activity			skin(3)|ovary(1)	4					Amineptine(DB04836)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Desipramine(DB01151)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Doxepin(DB01142)|Duloxetine(DB00476)|Escitalopram(DB01175)|Fluoxetine(DB00472)|Fluvoxamine(DB00176)|Imipramine(DB00458)|Methylphenidate(DB00422)|Milnacipran(DB04896)|Minaprine(DB00805)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Paroxetine(DB00715)|Phentermine(DB00191)|Protriptyline(DB00344)|Sertraline(DB01104)|Sibutramine(DB01105)|Tegaserod(DB01079)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Venlafaxine(DB00285)|Zimelidine(DB04832)													---	---	---	---
SUZ12	23512	broad.mit.edu	37	17	30320983	30320983	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30320983A>G	uc002hgs.2	+	12	1615	c.1393A>G	c.(1393-1395)AAG>GAG	p.K465E	SUZ12_uc002hgt.2_Missense_Mutation_p.K442E	NM_015355	NP_056170	Q15022	SUZ12_HUMAN	joined to JAZF1	465	C2H2-type.				negative regulation of cell differentiation|transcription, DNA-dependent	ESC/E(Z) complex	histone methyltransferase activity|methylated histone residue binding|zinc ion binding		JAZF1/SUZ12(131)	soft_tissue(98)|endometrium(33)	131		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.041)|Ovarian(249;0.182)|Breast(31;0.231)						T	JAZF1	endometrial stromal tumours								---	---	---	---
ACCN1	40	broad.mit.edu	37	17	32483443	32483443	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32483443G>A	uc002hhu.2	-	1	383	c.109C>T	c.(109-111)CCG>TCG	p.P37S		NM_001094	NP_001085	Q16515	ACCN1_HUMAN	amiloride-sensitive cation channel 1, neuronal	37	Cytoplasmic (By similarity).				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)													---	---	---	---
CCT6B	10693	broad.mit.edu	37	17	33266337	33266337	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33266337A>G	uc002hig.2	-	10	1172	c.1078T>C	c.(1078-1080)TTC>CTC	p.F360L	CCT6B_uc010ctg.2_Missense_Mutation_p.F323L|CCT6B_uc010wcc.1_Missense_Mutation_p.F315L	NM_006584	NP_006575	Q92526	TCPW_HUMAN	chaperonin containing TCP1, subunit 6B	360					chaperone-mediated protein complex assembly|protein folding|spermatogenesis	cytoplasm	ATP binding|protein transporter activity|unfolded protein binding			pancreas(1)	1		Ovarian(249;0.17)																---	---	---	---
MYO19	80179	broad.mit.edu	37	17	34861202	34861202	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34861202C>T	uc010wcy.1	-	20	2831	c.1839G>A	c.(1837-1839)ACG>ACA	p.T613T	MYO19_uc002hmw.2_Intron|MYO19_uc010cuu.2_RNA	NM_001163735	NP_001157207	Q96H55	MYO19_HUMAN	myosin XIX isoform 2	613	Myosin head-like.					mitochondrial outer membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)	1		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)														---	---	---	---
GPR179	440435	broad.mit.edu	37	17	36482651	36482651	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36482651G>A	uc002hpz.2	-	11	6822	c.6801C>T	c.(6799-6801)TTC>TTT	p.F2267F		NM_001004334	NP_001004334	Q6PRD1	GP179_HUMAN	GPR158-like 1 precursor	2267	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)																---	---	---	---
GPR179	440435	broad.mit.edu	37	17	36485372	36485372	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36485372C>A	uc002hpz.2	-	11	4101	c.4080G>T	c.(4078-4080)AAG>AAT	p.K1360N		NM_001004334	NP_001004334	Q6PRD1	GP179_HUMAN	GPR158-like 1 precursor	1360	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)																---	---	---	---
CWC25	54883	broad.mit.edu	37	17	36958336	36958336	+	3'UTR	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36958336G>T	uc002hqu.2	-	10					CWC25_uc010wdv.1_3'UTR|PIP4K2B_uc002hqs.2_5'Flank|PIP4K2B_uc010wdt.1_5'Flank	NM_017748	NP_060218			coiled-coil domain containing 49												0																		---	---	---	---
IKZF3	22806	broad.mit.edu	37	17	37922298	37922298	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37922298G>A	uc002hsu.2	-	8	1337	c.1275C>T	c.(1273-1275)TAC>TAT	p.Y425Y	IKZF3_uc002htd.2_Silent_p.Y391Y|IKZF3_uc010cwd.2_Silent_p.Y282Y|IKZF3_uc002hsv.2_Silent_p.Y352Y|IKZF3_uc010cwe.2_Silent_p.Y291Y|IKZF3_uc010cwf.2_Silent_p.Y243Y|IKZF3_uc010cwg.2_Silent_p.Y204Y|IKZF3_uc002hsw.2_Silent_p.Y386Y|IKZF3_uc002hsx.2_Silent_p.Y369Y|IKZF3_uc002hsy.2_Silent_p.Y386Y|IKZF3_uc002hsz.2_Silent_p.Y330Y|IKZF3_uc002hta.2_Silent_p.Y347Y|IKZF3_uc002htb.2_RNA|IKZF3_uc010cwh.2_Silent_p.Y338Y|IKZF3_uc002htc.2_Silent_p.Y178Y|IKZF3_uc010wel.1_Silent_p.Y178Y	NM_012481	NP_036613	Q9UKT9	IKZF3_HUMAN	aiolos isoform 1	425					B cell activation|mesoderm development|regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(2)|kidney(2)|skin(2)	6	Breast(7;4.5e-103)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)															---	---	---	---
MSL1	339287	broad.mit.edu	37	17	38290075	38290075	+	Intron	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38290075C>A	uc002hub.2	+						MSL1_uc002hua.3_Intron|MSL1_uc002hud.2_Intron	NM_001012241	NP_001012241			hampin						histone H4-K16 acetylation	MSL complex					0																		---	---	---	---
TNS4	84951	broad.mit.edu	37	17	38643296	38643296	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38643296C>T	uc010cxb.2	-	4	1444	c.1280G>A	c.(1279-1281)TGC>TAC	p.C427Y		NM_032865	NP_116254	Q8IZW8	TENS4_HUMAN	tensin 4 precursor	427					apoptosis|protein localization	cytoplasm|cytoskeleton|focal adhesion	actin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)															---	---	---	---
KRT33B	3884	broad.mit.edu	37	17	39525839	39525839	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39525839C>T	uc002hwl.2	-	1	209	c.164G>A	c.(163-165)AGC>AAC	p.S55N		NM_002279	NP_002270	Q14525	KT33B_HUMAN	type I hair keratin 3B	55	Head.					intermediate filament	protein binding|structural molecule activity				0		Breast(137;0.000496)																---	---	---	---
KRT14	3861	broad.mit.edu	37	17	39740625	39740625	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39740625C>T	uc002hxf.1	-	3	710	c.649G>A	c.(649-651)GAC>AAC	p.D217N	JUP_uc010wfs.1_Intron|KRT14_uc010cxp.1_Missense_Mutation_p.D217N	NM_000526	NP_000517	P02533	K1C14_HUMAN	keratin 14	217	Coil 1B.|Rod.				epidermis development|hemidesmosome assembly|intermediate filament bundle assembly	cytosol|keratin filament|mitochondrion|nucleus	protein binding|structural constituent of cytoskeleton			ovary(1)	1		Breast(137;0.000307)																---	---	---	---
CNP	1267	broad.mit.edu	37	17	40120095	40120095	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40120095T>G	uc002hyl.1	+	2	157	c.13T>G	c.(13-15)TTC>GTC	p.F5V	CNP_uc002hyk.1_Missense_Mutation_p.F5V|CNP_uc010wfz.1_Missense_Mutation_p.F5V|CNP_uc002hym.1_5'UTR|CNP_uc010wga.1_Intron	NM_033133	NP_149124	P09543	CN37_HUMAN	2',3'-cyclic nucleotide 3' phosphodiesterase	5					cell killing|cyclic nucleotide catabolic process|RNA metabolic process|synaptic transmission	extracellular space|melanosome	2',3'-cyclic-nucleotide 3'-phosphodiesterase activity|ATP binding|protein binding				0		all_cancers(22;2.38e-06)|all_epithelial(22;6.79e-05)|Breast(137;0.000143)		UCEC - Uterine corpus endometrioid carcinoma (308;0.171)														---	---	---	---
KAT2A	2648	broad.mit.edu	37	17	40272354	40272354	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40272354C>A	uc002hyx.2	-	3	558	c.498G>T	c.(496-498)GAG>GAT	p.E166D	HSPB9_uc002hyy.2_5'Flank	NM_021078	NP_066564	Q92830	KAT2A_HUMAN	general control of amino acid synthesis 5-like	166					chromatin remodeling|histone deubiquitination|interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex|STAGA complex|transcription factor TFTC complex	H3 histone acetyltransferase activity|histone deacetylase binding|protein binding|transcription coactivator activity			upper_aerodigestive_tract(1)|lung(1)	2																		---	---	---	---
EZH1	2145	broad.mit.edu	37	17	40858180	40858180	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40858180G>A	uc002iaz.2	-	16	1829	c.1684C>T	c.(1684-1686)CGC>TGC	p.R562C	EZH1_uc002iba.2_Missense_Mutation_p.R553C|EZH1_uc010wgt.1_Missense_Mutation_p.R492C|EZH1_uc010wgu.1_Missense_Mutation_p.R568C|EZH1_uc010wgv.1_Missense_Mutation_p.R522C|EZH1_uc010wgw.1_Missense_Mutation_p.R423C|EZH1_uc010cyp.2_Missense_Mutation_p.R463C|EZH1_uc010cyq.2_Missense_Mutation_p.R479C|EZH1_uc010cyo.1_Missense_Mutation_p.R225C	NM_001991	NP_001982	Q92800	EZH1_HUMAN	enhancer of zeste homolog 1	562	Cys-rich.				anatomical structure morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	chromatin binding|DNA binding			ovary(3)	3		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0784)														---	---	---	---
NBR1	4077	broad.mit.edu	37	17	41341709	41341709	+	Silent	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41341709C>A	uc010czd.2	+	8	725	c.585C>A	c.(583-585)GTC>GTA	p.V195V	NBR1_uc010diz.2_Silent_p.V195V|NBR1_uc010whu.1_Silent_p.V195V|NBR1_uc010whv.1_Silent_p.V195V|NBR1_uc010whw.1_Silent_p.V174V|NBR1_uc010whx.1_5'Flank	NM_031862	NP_114068	Q14596	NBR1_HUMAN	neighbor of BRCA1 gene 1	195					macroautophagy|protein oligomerization	autophagic vacuole|cytoplasmic vesicle|cytosol|late endosome|lysosome|sarcomere	ubiquitin binding|zinc ion binding			skin(1)	1		Breast(137;0.00086)		BRCA - Breast invasive adenocarcinoma(366;0.0934)														---	---	---	---
DUSP3	1845	broad.mit.edu	37	17	41846965	41846965	+	3'UTR	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41846965G>A	uc002ied.3	-	3					DUSP3_uc002iee.3_3'UTR|DUSP3_uc002ief.1_3'UTR	NM_004090	NP_004081			dual specificity phosphatase 3						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|negative regulation of JNK cascade|negative regulation of T cell activation|negative regulation of T cell receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of mitotic cell cycle|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|immunological synapse|nucleoplasm	MAP kinase phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0		Breast(137;0.00725)		BRCA - Breast invasive adenocarcinoma(366;0.116)														---	---	---	---
RUNDC3A	10900	broad.mit.edu	37	17	42390852	42390852	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42390852C>T	uc002igl.3	+	4	713	c.439C>T	c.(439-441)CGT>TGT	p.R147C	RUNDC3A_uc002igi.2_Missense_Mutation_p.R147C|RUNDC3A_uc002igj.2_Missense_Mutation_p.R142C|RUNDC3A_uc002igk.2_Missense_Mutation_p.R143C	NM_001144825	NP_001138297	Q59EK9	RUN3A_HUMAN	RUN domain containing 3A isoform 1	147	Interaction with RAP2A (By similarity).|RUN.				small GTPase mediated signal transduction		small GTPase regulator activity				0		Prostate(33;0.0233)		BRCA - Breast invasive adenocarcinoma(366;0.189)														---	---	---	---
RUNDC3A	10900	broad.mit.edu	37	17	42394857	42394857	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42394857C>T	uc002igl.3	+						RUNDC3A_uc002igi.2_Silent_p.S401S|RUNDC3A_uc002igj.2_Silent_p.S396S|RUNDC3A_uc002igk.2_Silent_p.S397S	NM_001144825	NP_001138297			RUN domain containing 3A isoform 1						small GTPase mediated signal transduction		small GTPase regulator activity				0		Prostate(33;0.0233)		BRCA - Breast invasive adenocarcinoma(366;0.189)														---	---	---	---
EFTUD2	9343	broad.mit.edu	37	17	42961031	42961031	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42961031G>T	uc002ihn.2	-	5	673	c.412C>A	c.(412-414)CTC>ATC	p.L138I	EFTUD2_uc010wje.1_Missense_Mutation_p.L103I|EFTUD2_uc010wjf.1_Missense_Mutation_p.L138I	NM_004247	NP_004238	Q15029	U5S1_HUMAN	elongation factor Tu GTP binding domain	138	GTP (Potential).					Cajal body|catalytic step 2 spliceosome|cytoplasm|nuclear speck	GTP binding|GTPase activity|protein binding			ovary(1)	1		Prostate(33;0.109)																---	---	---	---
CCDC103	388389	broad.mit.edu	37	17	42979811	42979811	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42979811C>T	uc002iho.2	+	4	438	c.355C>T	c.(355-357)CGC>TGC	p.R119C	EFTUD2_uc002ihn.2_5'Flank|EFTUD2_uc010wje.1_5'Flank|EFTUD2_uc010wjf.1_5'Flank|CCDC103_uc002ihp.1_5'Flank	NM_213607	NP_998772	Q8IW40	CC103_HUMAN	coiled-coil domain containing 103	119										kidney(1)	1		Prostate(33;0.109)																---	---	---	---
FMNL1	752	broad.mit.edu	37	17	43322257	43322257	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43322257C>T	uc002iin.2	+	20	2789	c.2589C>T	c.(2587-2589)AGC>AGT	p.S863S	FMNL1_uc002iiq.2_Silent_p.S441S|FMNL1_uc010dag.2_RNA	NM_005892	NP_005883	O95466	FMNL_HUMAN	formin-like 1	863	FH2.				actin cytoskeleton organization		actin binding|Rho GTPase binding			pancreas(1)	1																		---	---	---	---
C17orf57	124989	broad.mit.edu	37	17	45481982	45481982	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45481982A>C	uc002iln.2	+	20	2627	c.2216A>C	c.(2215-2217)AAA>ACA	p.K739T	C17orf57_uc002ilm.2_Missense_Mutation_p.K643T	NM_152347	NP_689560	Q8IY85	CQ057_HUMAN	hypothetical protein LOC124989	739							calcium ion binding			breast(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
HOXB2	3212	broad.mit.edu	37	17	46620554	46620554	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46620554A>G	uc002inm.2	-	2	1067	c.947T>C	c.(946-948)CTC>CCC	p.L316P		NM_002145	NP_002136	P14652	HXB2_HUMAN	homeobox B2	316					blood circulation	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
MYST2	11143	broad.mit.edu	37	17	47888865	47888865	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47888865A>G	uc002ipm.2	+	7	907	c.781A>G	c.(781-783)AAG>GAG	p.K261E	MYST2_uc002ipl.1_Missense_Mutation_p.K231E|MYST2_uc010wma.1_Missense_Mutation_p.K122E|MYST2_uc010wmb.1_Missense_Mutation_p.K151E|MYST2_uc010wmc.1_Missense_Mutation_p.K92E|MYST2_uc010wmd.1_Missense_Mutation_p.K105E|MYST2_uc010wme.1_Missense_Mutation_p.K75E	NM_007067	NP_008998	O95251	MYST2_HUMAN	MYST histone acetyltransferase 2	261					DNA replication|histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	histone acetyltransferase activity|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
CACNA1G	8913	broad.mit.edu	37	17	48681583	48681583	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48681583G>A	uc002irk.1	+	22	4609	c.4237G>A	c.(4237-4239)GGC>AGC	p.G1413S	CACNA1G_uc002iri.1_Missense_Mutation_p.G1413S|CACNA1G_uc002irj.1_Missense_Mutation_p.G1390S|CACNA1G_uc002irl.1_Missense_Mutation_p.G1390S|CACNA1G_uc002irm.1_Missense_Mutation_p.G1390S|CACNA1G_uc002irn.1_Missense_Mutation_p.G1390S|CACNA1G_uc002iro.1_Missense_Mutation_p.G1390S|CACNA1G_uc002irp.1_Missense_Mutation_p.G1413S|CACNA1G_uc002irq.1_Missense_Mutation_p.G1390S|CACNA1G_uc002irr.1_Missense_Mutation_p.G1413S|CACNA1G_uc002irs.1_Missense_Mutation_p.G1413S|CACNA1G_uc002irt.1_Missense_Mutation_p.G1413S|CACNA1G_uc002irv.1_Missense_Mutation_p.G1413S|CACNA1G_uc002irw.1_Missense_Mutation_p.G1390S|CACNA1G_uc002iru.1_Missense_Mutation_p.G1390S|CACNA1G_uc002irx.1_Missense_Mutation_p.G1326S|CACNA1G_uc002iry.1_Missense_Mutation_p.G1326S|CACNA1G_uc002irz.1_Missense_Mutation_p.G1326S|CACNA1G_uc002isa.1_Missense_Mutation_p.G1326S|CACNA1G_uc002isb.1_Missense_Mutation_p.G1326S|CACNA1G_uc002isc.1_Missense_Mutation_p.G1326S|CACNA1G_uc002isd.1_Missense_Mutation_p.G1326S|CACNA1G_uc002ise.1_Missense_Mutation_p.G1326S|CACNA1G_uc002isf.1_Missense_Mutation_p.G1326S|CACNA1G_uc002isg.1_Missense_Mutation_p.G1326S|CACNA1G_uc002ish.1_Missense_Mutation_p.G1326S|CACNA1G_uc002isi.1_Missense_Mutation_p.G1303S|CACNA1G_uc002isj.2_Missense_Mutation_p.G137S	NM_018896	NP_061496	O43497	CAC1G_HUMAN	voltage-dependent calcium channel alpha 1G	1413	Helical; Name=S5 of repeat III; (Potential).|III.				axon guidance	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(1)	1	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Ethosuximide(DB00593)|Flunarizine(DB04841)|Levetiracetam(DB01202)|Mibefradil(DB01388)|Pimozide(DB01100)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)													---	---	---	---
CACNA1G	8913	broad.mit.edu	37	17	48696021	48696021	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48696021C>T	uc002irk.1	+	33	5805	c.5433C>T	c.(5431-5433)ACC>ACT	p.T1811T	CACNA1G_uc002irj.1_Silent_p.T1777T|CACNA1G_uc002irl.1_Silent_p.T1788T|CACNA1G_uc002irm.1_Silent_p.T1777T|CACNA1G_uc002irn.1_Silent_p.T1770T|CACNA1G_uc002iro.1_Silent_p.T1777T|CACNA1G_uc002irp.1_Silent_p.T1811T|CACNA1G_uc002irq.1_Silent_p.T1788T|CACNA1G_uc002irr.1_Silent_p.T1811T|CACNA1G_uc002irs.1_Silent_p.T1800T|CACNA1G_uc002irt.1_Silent_p.T1793T|CACNA1G_uc002irv.1_Silent_p.T1800T|CACNA1G_uc002irw.1_Silent_p.T1788T|CACNA1G_uc002iru.1_Silent_p.T1777T|CACNA1G_uc002irx.1_Silent_p.T1724T|CACNA1G_uc002iry.1_Silent_p.T1713T|CACNA1G_uc002irz.1_Silent_p.T1717T|CACNA1G_uc002isa.1_Silent_p.T1690T|CACNA1G_uc002isb.1_Silent_p.T1731T|CACNA1G_uc002isc.1_Silent_p.T1713T|CACNA1G_uc002isd.1_Silent_p.T1699T|CACNA1G_uc002ise.1_Silent_p.T1679T|CACNA1G_uc002isf.1_Silent_p.T1706T|CACNA1G_uc002isg.1_Silent_p.T1672T|CACNA1G_uc002ish.1_Silent_p.T1679T|CACNA1G_uc002isi.1_Silent_p.T1667T	NM_018896	NP_061496	O43497	CAC1G_HUMAN	voltage-dependent calcium channel alpha 1G	1811	IV.|Extracellular (Potential).				axon guidance	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(1)	1	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Ethosuximide(DB00593)|Flunarizine(DB04841)|Levetiracetam(DB01202)|Mibefradil(DB01388)|Pimozide(DB01100)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)													---	---	---	---
SPAG9	9043	broad.mit.edu	37	17	49072478	49072478	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49072478T>A	uc002itc.2	-	18	2375	c.2166A>T	c.(2164-2166)GAA>GAT	p.E722D	SPAG9_uc002itb.2_Missense_Mutation_p.E708D|SPAG9_uc002itd.2_Missense_Mutation_p.E712D|SPAG9_uc002itf.2_Missense_Mutation_p.E543D|SPAG9_uc002ita.2_Missense_Mutation_p.E565D|SPAG9_uc002ite.2_Missense_Mutation_p.E552D	NM_001130528	NP_001124000	O60271	JIP4_HUMAN	sperm associated antigen 9 isoform 1	722					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)															---	---	---	---
CA10	56934	broad.mit.edu	37	17	49825097	49825097	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49825097G>A	uc002itw.3	-	4	1347	c.361C>T	c.(361-363)CCC>TCC	p.P121S	CA10_uc002itu.3_Missense_Mutation_p.P50S|CA10_uc002itv.3_Missense_Mutation_p.P127S|CA10_uc002itx.3_Missense_Mutation_p.P121S|CA10_uc002ity.3_Missense_Mutation_p.P121S|CA10_uc002itz.2_Missense_Mutation_p.P121S	NM_020178	NP_064563	Q9NS85	CAH10_HUMAN	carbonic anhydrase X	121					brain development					ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)															---	---	---	---
TMEM100	55273	broad.mit.edu	37	17	53798336	53798336	+	Silent	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53798336G>T	uc002iuj.3	-	2	407	c.96C>A	c.(94-96)ACC>ACA	p.T32T	TMEM100_uc002iuk.3_Silent_p.T32T	NM_018286	NP_060756	Q9NV29	TM100_HUMAN	transmembrane protein 100	32						integral to membrane					0																		---	---	---	---
ANKFN1	162282	broad.mit.edu	37	17	54534704	54534704	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54534704A>G	uc002iun.1	+	12	1438	c.1403A>G	c.(1402-1404)GAC>GGC	p.D468G		NM_153228	NP_694960	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain	468										large_intestine(1)|ovary(1)	2																		---	---	---	---
BZRAP1	9256	broad.mit.edu	37	17	56386556	56386556	+	Silent	SNP	C	T	T	rs150791088		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56386556C>T	uc002ivx.3	-	22	4948	c.4077G>A	c.(4075-4077)CCG>CCA	p.P1359P	BZRAP1_uc002ivw.2_5'Flank|BZRAP1_uc010dcs.2_Silent_p.P1299P|BZRAP1_uc010wnt.1_Silent_p.P1359P	NM_004758	NP_004749	O95153	RIMB1_HUMAN	peripheral benzodiazepine receptor-associated	1359						mitochondrion	benzodiazepine receptor binding			upper_aerodigestive_tract(2)|skin(1)	3	Medulloblastoma(34;0.127)|all_neural(34;0.237)																	---	---	---	---
TEX14	56155	broad.mit.edu	37	17	56707864	56707864	+	Missense_Mutation	SNP	G	A	A	rs141835848	byFrequency	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56707864G>A	uc010dcz.1	-	3	306	c.188C>T	c.(187-189)GCG>GTG	p.A63V	TEX14_uc002iwr.1_Missense_Mutation_p.A63V|TEX14_uc002iws.1_Missense_Mutation_p.A63V|TEX14_uc010dda.1_5'UTR	NM_198393	NP_938207	Q8IWB6	TEX14_HUMAN	testis expressed sequence 14 isoform a	63	ANK 2.					cytoplasm	ATP binding|protein kinase activity			stomach(4)|lung(3)|breast(3)|ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)|pancreas(1)	17	Medulloblastoma(34;0.127)|all_neural(34;0.237)																	---	---	---	---
TLK2	11011	broad.mit.edu	37	17	60558548	60558548	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60558548C>A	uc010ddp.2	+	2	330	c.62C>A	c.(61-63)ACT>AAT	p.T21N	TLK2_uc002izx.3_Translation_Start_Site|TLK2_uc002izz.3_Missense_Mutation_p.T21N|TLK2_uc002jaa.3_Missense_Mutation_p.T21N|TLK2_uc010wpd.1_Missense_Mutation_p.T21N	NM_006852	NP_006843	Q86UE8	TLK2_HUMAN	tousled-like kinase 2 isoform A	21					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																		---	---	---	---
CCDC46	201134	broad.mit.edu	37	17	63898359	63898359	+	Missense_Mutation	SNP	G	A	A	rs149561928	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63898359G>A	uc002jfl.2	-	20	2293	c.2074C>T	c.(2074-2076)CGG>TGG	p.R692W	CCDC46_uc010deo.2_Missense_Mutation_p.R434W|CCDC46_uc002jfm.2_Missense_Mutation_p.R692W|CCDC46_uc010dep.2_Missense_Mutation_p.R650W	NM_145036	NP_659473	Q8N8E3	CE112_HUMAN	coiled-coil domain containing 46 isoform a	692	Potential.					centrosome					0			BRCA - Breast invasive adenocarcinoma(6;1.53e-06)															---	---	---	---
HELZ	9931	broad.mit.edu	37	17	65105440	65105440	+	Silent	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65105440G>T	uc010wqk.1	-	29	4471	c.4284C>A	c.(4282-4284)CCC>CCA	p.P1428P	HELZ_uc002jfv.3_RNA|HELZ_uc002jfx.3_Silent_p.P1427P|HELZ_uc010der.2_5'UTR	NM_014877	NP_055692			helicase with zinc finger domain											ovary(1)|pancreas(1)	2	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)																	---	---	---	---
ABCA9	10350	broad.mit.edu	37	17	66979874	66979874	+	Missense_Mutation	SNP	A	G	G	rs150959606		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66979874A>G	uc002jhu.2	-	36	4759	c.4616T>C	c.(4615-4617)TTC>TCC	p.F1539S	ABCA9_uc010dez.2_Missense_Mutation_p.F1501S	NM_080283	NP_525022	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A, member 9	1539					transport	integral to membrane	ATP binding|ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)	6	Breast(10;1.47e-12)																	---	---	---	---
C17orf80	55028	broad.mit.edu	37	17	71232725	71232725	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71232725A>G	uc002jjm.3	+	3	1298	c.1104A>G	c.(1102-1104)GTA>GTG	p.V368V	C17orf80_uc010wqu.1_Silent_p.V368V|C17orf80_uc010dfj.2_Silent_p.V368V|C17orf80_uc002jjk.1_Silent_p.V368V|C17orf80_uc002jjl.3_Silent_p.V368V	NM_017941	NP_060411	Q9BSJ5	CQ080_HUMAN	lung cancer-related protein 8 isoform a	368	Extracellular (Potential).					integral to membrane				skin(1)	1			LUSC - Lung squamous cell carcinoma(166;0.197)															---	---	---	---
RECQL5	9400	broad.mit.edu	37	17	73659071	73659071	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73659071C>T	uc010dgl.2	-	4	415	c.259G>A	c.(259-261)GTG>ATG	p.V87M	RECQL5_uc010dgk.2_Missense_Mutation_p.V60M|RECQL5_uc002jpb.1_Missense_Mutation_p.V87M|RECQL5_uc002joz.3_Missense_Mutation_p.V87M|RECQL5_uc002jpa.3_Missense_Mutation_p.V87M	NM_004259	NP_004250	O94762	RECQ5_HUMAN	RecQ protein-like 5 isoform 1	87	Helicase ATP-binding.				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					---	---	---	---
CDK3	1018	broad.mit.edu	37	17	73999441	73999441	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73999441G>A	uc010dgt.2	+	7	830	c.754G>A	c.(754-756)GTG>ATG	p.V252M	CDK3_uc002jqg.3_Missense_Mutation_p.V280M	NM_001258	NP_001249	Q00526	CDK3_HUMAN	cyclin-dependent kinase 3	252	Protein kinase.				cell division|cell proliferation|mitosis		ATP binding|cyclin-dependent protein kinase activity			central_nervous_system(1)	1																		---	---	---	---
UBE2O	63893	broad.mit.edu	37	17	74393912	74393912	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74393912C>T	uc002jrm.3	-	13	2148	c.2083G>A	c.(2083-2085)GCT>ACT	p.A695T	UBE2O_uc002jrn.3_Missense_Mutation_p.A695T|UBE2O_uc002jrl.3_Missense_Mutation_p.A299T	NM_022066	NP_071349	Q9C0C9	UBE2O_HUMAN	ubiquitin-conjugating enzyme E2O	695							ATP binding|ubiquitin-protein ligase activity			breast(2)|skin(2)|lung(1)	5																OREG0024751	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SEPT9	10801	broad.mit.edu	37	17	75484817	75484817	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75484817C>A	uc002jts.3	+	7	1259	c.1133C>A	c.(1132-1134)CCC>CAC	p.P378H	SEPT9_uc010wtk.1_Missense_Mutation_p.P359H|SEPT9_uc002jtt.3_Missense_Mutation_p.P214H|SEPT9_uc002jtu.3_Missense_Mutation_p.P360H|SEPT9_uc002jtv.2_Missense_Mutation_p.P371H|SEPT9_uc002jtw.2_Missense_Mutation_p.P214H|SEPT9_uc010wtl.1_Missense_Mutation_p.P154H|SEPT9_uc002jty.3_Missense_Mutation_p.P127H|SEPT9_uc010wtm.1_Missense_Mutation_p.P127H|SEPT9_uc010wtn.1_Missense_Mutation_p.P127H|SEPT9_uc010dhd.2_Missense_Mutation_p.P266H	NM_001113491	NP_001106963	Q9UHD8	SEPT9_HUMAN	septin 9 isoform a	378					cell cycle|cell division|protein heterooligomerization	microtubule|perinuclear region of cytoplasm|stress fiber	GTP binding|GTPase activity|protein binding|protein binding			breast(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(99;0.153)															---	---	---	---
TK1	7083	broad.mit.edu	37	17	76178741	76178741	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76178741C>T	uc002juw.2	-	4	442	c.232G>A	c.(232-234)GCC>ACC	p.A78T	TK1_uc002jux.2_Missense_Mutation_p.A120T	NM_003258	NP_003249	P04183	KITH_HUMAN	thymidine kinase 1	78					DNA replication|protein homotetramerization|pyrimidine base metabolic process|pyrimidine nucleoside salvage	cytosol	ATP binding|thymidine kinase activity|zinc ion binding				0			BRCA - Breast invasive adenocarcinoma(99;0.00269)|OV - Ovarian serous cystadenocarcinoma(97;0.0804)|Lung(188;0.23)															---	---	---	---
DNAH17	8632	broad.mit.edu	37	17	76455154	76455154	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76455154C>T	uc010dhp.1	-	6	1012	c.790G>A	c.(790-792)GCA>ACA	p.A264T	DNAH17_uc002jvs.2_RNA					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)															---	---	---	---
ENGASE	64772	broad.mit.edu	37	17	77076392	77076392	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77076392C>G	uc002jwv.2	+	5	677	c.669C>G	c.(667-669)ATC>ATG	p.I223M	ENGASE_uc002jwu.1_Missense_Mutation_p.I223M|ENGASE_uc010wtz.1_Missense_Mutation_p.I37M|ENGASE_uc002jww.2_Translation_Start_Site	NM_001042573	NP_001036038	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	223						cytosol	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity			skin(1)	1																		---	---	---	---
SLC26A11	284129	broad.mit.edu	37	17	78196512	78196512	+	Missense_Mutation	SNP	G	T	T	rs139873166		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78196512G>T	uc002jyb.1	+	4	562	c.293G>T	c.(292-294)CGG>CTG	p.R98L	SGSH_uc002jxz.3_5'Flank|SGSH_uc002jya.3_5'Flank|SGSH_uc002jxy.2_5'Flank|SGSH_uc010wue.1_5'Flank|SLC26A11_uc002jyc.1_Missense_Mutation_p.R98L|SLC26A11_uc002jyd.1_Missense_Mutation_p.R98L|SLC26A11_uc010dhv.1_Missense_Mutation_p.R98L	NM_173626	NP_775897	Q86WA9	S2611_HUMAN	solute carrier family 26, member 11	98	Extracellular (Potential).					endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosomal membrane|plasma membrane	anion:anion antiporter activity|secondary active sulfate transmembrane transporter activity				0	all_neural(118;0.0538)		OV - Ovarian serous cystadenocarcinoma(97;0.0344)|BRCA - Breast invasive adenocarcinoma(99;0.0908)															---	---	---	---
NOTUM	147111	broad.mit.edu	37	17	79914807	79914807	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79914807A>G	uc010wvg.1	-	7	1111	c.839T>C	c.(838-840)GTC>GCC	p.V280A		NM_178493	NP_848588	Q6P988	NOTUM_HUMAN	notum pectinacetylesterase homolog precursor	280						extracellular region	hydrolase activity				0	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)															---	---	---	---
ASPSCR1	79058	broad.mit.edu	37	17	79973226	79973226	+	Intron	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79973226A>G	uc002kcx.2	+						ASPSCR1_uc002kcw.1_Intron|ASPSCR1_uc002kcy.2_Silent_p.T543T|ASPSCR1_uc002kcz.2_Intron|ASPSCR1_uc002kda.2_Intron	NM_024083	NP_076988			alveolar soft part sarcoma chromosome region,								protein binding		ASPSCR1/TFE3(161)	soft_tissue(118)|kidney(43)|breast(1)	162	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)					T	TFE3	alveolar soft part sarcoma								---	---	---	---
TBCD	6904	broad.mit.edu	37	17	80758854	80758854	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80758854C>T	uc002kfz.2	+	9	1062	c.932C>T	c.(931-933)CCG>CTG	p.P311L	TBCD_uc002kfx.1_Missense_Mutation_p.P294L|TBCD_uc002kfy.1_Missense_Mutation_p.P311L	NM_005993	NP_005984	Q9BTW9	TBCD_HUMAN	beta-tubulin cofactor D	311					'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)															---	---	---	---
CLUL1	27098	broad.mit.edu	37	18	624919	624919	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:624919C>T	uc002kkp.2	+	4	455	c.310C>T	c.(310-312)CTA>TTA	p.L104L	CLUL1_uc010wys.1_Silent_p.L156L|CLUL1_uc002kkq.2_Silent_p.L104L	NM_014410	NP_055225	Q15846	CLUL1_HUMAN	clusterin-like 1 (retinal) precursor	104	Potential.				cell death	extracellular region				ovary(2)	2																		---	---	---	---
TGIF1	7050	broad.mit.edu	37	18	3452047	3452047	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3452047G>T	uc002klz.2	+	1	457	c.70G>T	c.(70-72)GGC>TGC	p.G24C	TGIF1_uc002klu.2_Intron|TGIF1_uc002klv.2_Intron|TGIF1_uc002klx.2_Intron|TGIF1_uc002klw.2_Intron|TGIF1_uc010dkm.1_Intron|TGIF1_uc002kly.2_Intron|TGIF1_uc002kma.2_Intron|TGIF1_uc002kmb.2_5'Flank	NM_170695	NP_733796	Q15583	TGIF1_HUMAN	TG-interacting factor isoform a	24					negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1	Esophageal squamous(4;0.0859)	Colorectal(8;0.0104)																---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	3879898	3879898	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3879898G>A	uc002kmf.2	-	1	238	c.171C>T	c.(169-171)TGC>TGT	p.C57C	DLGAP1_uc010wyz.1_Silent_p.C57C|DLGAP1_uc002kmk.2_Silent_p.C57C|uc002kml.1_Intron	NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform	57					synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
ANKRD12	23253	broad.mit.edu	37	18	9257815	9257815	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9257815A>G	uc002knv.2	+	9	4807	c.4550A>G	c.(4549-4551)CAA>CGA	p.Q1517R	ANKRD12_uc002knw.2_Missense_Mutation_p.Q1494R|ANKRD12_uc002knx.2_Missense_Mutation_p.Q1494R|ANKRD12_uc010dkx.1_Missense_Mutation_p.Q1224R	NM_015208	NP_056023	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12 isoform 1	1517						nucleus				ovary(2)|central_nervous_system(1)	3																		---	---	---	---
TXNDC2	84203	broad.mit.edu	37	18	9887721	9887721	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9887721G>T	uc002koi.3	+	2	1694	c.1245G>T	c.(1243-1245)AAG>AAT	p.K415N	TXNDC2_uc010wzq.1_RNA|TXNDC2_uc002koh.3_Missense_Mutation_p.K348N	NM_001098529	NP_001091999	Q86VQ3	TXND2_HUMAN	thioredoxin domain-containing 2 isoform 2	415	21.|22 X 15 AA approximate tandem repeat of Q-P-K-X-G-D-I-P-K-S-[PS]-E-[KE]-X-I.				cell differentiation|cell redox homeostasis|glycerol ether metabolic process|multicellular organismal development|spermatogenesis	cytoplasm	electron carrier activity|nutrient reservoir activity|protein disulfide oxidoreductase activity|thioredoxin-disulfide reductase activity			ovary(1)|pancreas(1)	2																		---	---	---	---
APCDD1	147495	broad.mit.edu	37	18	10485592	10485592	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10485592G>A	uc002kom.3	+	4	1262	c.908G>A	c.(907-909)CGC>CAC	p.R303H		NM_153000	NP_694545	Q8J025	APCD1_HUMAN	adenomatosis polyposis coli down-regulated 1	303	Extracellular (Potential).				hair follicle development|negative regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to plasma membrane	Wnt-protein binding				0				READ - Rectum adenocarcinoma(15;0.08)														---	---	---	---
FAM38B	63895	broad.mit.edu	37	18	10671570	10671570	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10671570C>T	uc002kor.3	-	14	2224	c.2084G>A	c.(2083-2085)CGC>CAC	p.R695H	FAM38B_uc002koq.2_Missense_Mutation_p.R530H	NM_022068	NP_071351	Q9H5I5	PIEZ2_HUMAN	family with sequence similarity 38, member B	2738						integral to membrane	ion channel activity			ovary(1)	1																		---	---	---	---
MC5R	4161	broad.mit.edu	37	18	13826359	13826359	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13826359T>C	uc010xaf.1	+	1	595	c.595T>C	c.(595-597)TTC>CTC	p.F199L		NM_005913	NP_005904	P33032	MC5R_HUMAN	melanocortin 5 receptor	199	Helical; Name=5; (Potential).				G-protein signaling, coupled to cyclic nucleotide second messenger|positive regulation of cAMP biosynthetic process	integral to plasma membrane	melanocortin receptor activity|protein binding			ovary(3)|lung(2)|breast(1)	6																		---	---	---	---
B4GALT6	9331	broad.mit.edu	37	18	29210931	29210931	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29210931T>C	uc002kwz.3	-	6	1064	c.767A>G	c.(766-768)TAC>TGC	p.Y256C	B4GALT6_uc010dma.2_Missense_Mutation_p.Y217C|B4GALT6_uc010dmb.2_Missense_Mutation_p.Y217C	NM_004775	NP_004766	Q9UBX8	B4GT6_HUMAN	beta-1,4-galactosyltransferase 6	256	Lumenal (Potential).				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)															---	---	---	---
ZNF396	252884	broad.mit.edu	37	18	32954091	32954091	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32954091T>C	uc010xcf.1	-	2	298	c.166A>G	c.(166-168)AGG>GGG	p.R56G		NM_145756	NP_665699	Q96N95	ZN396_HUMAN	zinc finger protein 396	56	SCAN box.				viral reproduction	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
GALNT1	2589	broad.mit.edu	37	18	33271100	33271100	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33271100G>A	uc010dmu.2	+	8	1156	c.1103G>A	c.(1102-1104)CGA>CAA	p.R368Q	GALNT1_uc002kyz.3_Missense_Mutation_p.R308Q|GALNT1_uc002kzb.2_Missense_Mutation_p.R368Q	NM_020474	NP_065207	Q10472	GALT1_HUMAN	polypeptide N-acetylgalactosaminyltransferase 1	368	Lumenal (Potential).				protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	extracellular region|Golgi cisterna membrane|integral to membrane|perinuclear region of cytoplasm	manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)	2																		---	---	---	---
RIT2	6014	broad.mit.edu	37	18	40503582	40503582	+	Silent	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40503582G>T	uc002lav.2	-	4	554	c.381C>A	c.(379-381)CCC>CCA	p.P127P	RIT2_uc010dnf.2_Silent_p.P127P	NM_002930	NP_002921	Q99578	RIT2_HUMAN	Ras-like without CAAX 2	127					nerve growth factor receptor signaling pathway|small GTPase mediated signal transduction|synaptic transmission	intracellular|plasma membrane	calmodulin binding|GTP binding|GTPase activity			ovary(1)	1																		---	---	---	---
TCEB3C	162699	broad.mit.edu	37	18	44555207	44555207	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44555207G>A	uc010xdb.1	-	1	1243	c.1007C>T	c.(1006-1008)ACG>ATG	p.T336M	KATNAL2_uc010dnq.1_Intron|KATNAL2_uc002lco.2_Intron|KATNAL2_uc002lcp.3_Intron	NM_145653	NP_663628	Q8NG57	ELOA3_HUMAN	transcription elongation factor B polypeptide	336	Interaction with elongin BC (By similarity).|Activation domain (By similarity).				regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane|nucleus	DNA binding				0																		---	---	---	---
SMAD2	4087	broad.mit.edu	37	18	45375016	45375016	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45375016G>A	uc002lcy.2	-	8	1075	c.827C>T	c.(826-828)TCG>TTG	p.S276L	SMAD2_uc002lcz.2_Missense_Mutation_p.S276L|SMAD2_uc010xdc.1_Missense_Mutation_p.S246L|SMAD2_uc010xdd.1_Missense_Mutation_p.S246L	NM_005901	NP_005892	Q15796	SMAD2_HUMAN	Sma- and Mad-related protein 2 isoform 1	276	MH2.				anterior/posterior pattern formation|cell fate commitment|common-partner SMAD protein phosphorylation|intracellular signal transduction|mesoderm formation|negative regulation of transcription, DNA-dependent|palate development|paraxial mesoderm morphogenesis|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription from RNA polymerase II promoter|primary miRNA processing|regulation of binding|regulation of transforming growth factor beta receptor signaling pathway|response to cholesterol|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway|zygotic specification of dorsal/ventral axis	activin responsive factor complex|cytosol	activating transcription factor binding|co-SMAD binding|double-stranded DNA binding|I-SMAD binding|R-SMAD binding|sequence-specific DNA binding transcription factor activity|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity|type I transforming growth factor beta receptor binding|ubiquitin protein ligase binding			large_intestine(3)|lung(1)|central_nervous_system(1)	5																		---	---	---	---
SMAD2	4087	broad.mit.edu	37	18	45396844	45396844	+	Splice_Site	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45396844A>G	uc002lcy.2	-	3	574	c.326_splice	c.e3+1	p.R109_splice	SMAD2_uc002lcz.2_Splice_Site_p.R109_splice|SMAD2_uc010xdc.1_Intron|SMAD2_uc010xdd.1_Intron	NM_005901	NP_005892			Sma- and Mad-related protein 2 isoform 1						anterior/posterior pattern formation|cell fate commitment|common-partner SMAD protein phosphorylation|intracellular signal transduction|mesoderm formation|negative regulation of transcription, DNA-dependent|palate development|paraxial mesoderm morphogenesis|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription from RNA polymerase II promoter|primary miRNA processing|regulation of binding|regulation of transforming growth factor beta receptor signaling pathway|response to cholesterol|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway|zygotic specification of dorsal/ventral axis	activin responsive factor complex|cytosol	activating transcription factor binding|co-SMAD binding|double-stranded DNA binding|I-SMAD binding|R-SMAD binding|sequence-specific DNA binding transcription factor activity|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity|type I transforming growth factor beta receptor binding|ubiquitin protein ligase binding			large_intestine(3)|lung(1)|central_nervous_system(1)	5																		---	---	---	---
LIPG	9388	broad.mit.edu	37	18	47101948	47101948	+	Missense_Mutation	SNP	A	G	G	rs150990240		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47101948A>G	uc002ldv.2	+	5	1033	c.781A>G	c.(781-783)ATT>GTT	p.I261V	LIPG_uc002ldu.1_Missense_Mutation_p.I261V|LIPG_uc010xdh.1_Intron	NM_006033	NP_006024	Q9Y5X9	LIPE_HUMAN	endothelial lipase precursor	261					cholesterol homeostasis|high-density lipoprotein particle remodeling|phospholipid catabolic process|phospholipid homeostasis|positive regulation of cholesterol transport|positive regulation of high-density lipoprotein particle clearance|reverse cholesterol transport	extracellular space	heparin binding|lipoprotein lipase activity|phospholipase A1 activity|protein binding|triglyceride lipase activity			ovary(1)|skin(1)	2																		---	---	---	---
MEX3C	51320	broad.mit.edu	37	18	48702831	48702831	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48702831C>T	uc002lfc.3	-	2	1870	c.1870G>A	c.(1870-1872)GGC>AGC	p.G624S		NM_016626	NP_057710	Q5U5Q3	MEX3C_HUMAN	ring finger and KH domain containing 2	624	RING-type.					cytoplasm|nucleus	RNA binding|zinc ion binding			lung(2)|ovary(1)|skin(1)	4		Colorectal(6;0.003)|all_epithelial(6;0.0473)		Colorectal(16;0.0175)|READ - Rectum adenocarcinoma(32;0.15)														---	---	---	---
NEDD4L	23327	broad.mit.edu	37	18	55998088	55998088	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55998088T>C	uc002lgy.2	+	11	1206	c.932T>C	c.(931-933)CTA>CCA	p.L311P	NEDD4L_uc002lgz.2_Missense_Mutation_p.L311P|NEDD4L_uc002lgx.2_Missense_Mutation_p.L311P|NEDD4L_uc010xee.1_Missense_Mutation_p.L190P|NEDD4L_uc002lhc.2_Missense_Mutation_p.L303P|NEDD4L_uc002lhd.2_Missense_Mutation_p.L190P|NEDD4L_uc002lhb.2_Missense_Mutation_p.L190P|NEDD4L_uc002lhe.2_Missense_Mutation_p.L303P|NEDD4L_uc002lhf.2_Missense_Mutation_p.L190P|NEDD4L_uc002lhg.2_Missense_Mutation_p.L190P|NEDD4L_uc002lhh.2_Missense_Mutation_p.L190P|NEDD4L_uc010dpm.1_Missense_Mutation_p.L162P	NM_001144967	NP_001138439	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally	311					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																		---	---	---	---
TNFRSF11A	8792	broad.mit.edu	37	18	60036114	60036114	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60036114G>A	uc002lin.2	+	9	1002	c.964G>A	c.(964-966)GAA>AAA	p.E322K	TNFRSF11A_uc010dpv.2_Intron	NM_003839	NP_003830	Q9Y6Q6	TNR11_HUMAN	tumor necrosis factor receptor superfamily,	322	Cytoplasmic (Potential).				adaptive immune response|cell-cell signaling|circadian temperature homeostasis|monocyte chemotaxis|osteoclast differentiation|positive regulation of cell proliferation|positive regulation of ERK1 and ERK2 cascade via TNFSF11-mediated signaling|positive regulation of fever generation by positive regulation of prostaglandin secretion|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|response to interleukin-1|response to lipopolysaccharide	external side of plasma membrane|integral to membrane	metal ion binding|tumor necrosis factor receptor activity			breast(2)|lung(1)	3		Colorectal(73;0.188)												Paget_Disease_of_Bone				---	---	---	---
DSEL	92126	broad.mit.edu	37	18	65178489	65178489	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65178489A>G	uc002lke.1	-	2	4611	c.3387T>C	c.(3385-3387)CCT>CCC	p.P1129P		NM_032160	NP_115536	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	1119						integral to membrane	isomerase activity|sulfotransferase activity			ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	6		Esophageal squamous(42;0.129)																---	---	---	---
TMX3	54495	broad.mit.edu	37	18	66365248	66365248	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66365248G>A	uc002lkf.2	-	7	548	c.413C>T	c.(412-414)CCA>CTA	p.P138L	TMX3_uc010xez.1_5'UTR|TMX3_uc010xfa.1_Missense_Mutation_p.P111L|TMX3_uc002lkg.3_Missense_Mutation_p.P138L	NM_019022	NP_061895	Q96JJ7	TMX3_HUMAN	thioredoxin domain containing 10 precursor	138	Lumenal (Potential).				cell redox homeostasis|glycerol ether metabolic process	endoplasmic reticulum membrane|integral to membrane	electron carrier activity|protein disulfide isomerase activity|protein disulfide oxidoreductase activity			skin(1)	1																		---	---	---	---
ZNF236	7776	broad.mit.edu	37	18	74637450	74637450	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74637450G>A	uc002lmi.2	+	22	4159	c.3961G>A	c.(3961-3963)GAT>AAT	p.D1321N	ZNF236_uc002lmj.2_RNA	NM_007345	NP_031371	Q9UL36	ZN236_HUMAN	zinc finger protein 236	1321					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)														---	---	---	---
NFATC1	4772	broad.mit.edu	37	18	77193648	77193648	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77193648G>A	uc010xfg.1	+	3	1749	c.1296G>A	c.(1294-1296)GTG>GTA	p.V432V	NFATC1_uc002lnc.1_Silent_p.V432V|NFATC1_uc010xff.1_Silent_p.V432V|NFATC1_uc002lnd.2_Silent_p.V432V|NFATC1_uc002lne.2_5'UTR|NFATC1_uc010xfh.1_Silent_p.V432V|NFATC1_uc010xfi.1_Silent_p.V419V|NFATC1_uc010xfj.1_5'UTR|NFATC1_uc002lnf.2_Silent_p.V419V|NFATC1_uc002lng.2_Silent_p.V419V|NFATC1_uc010xfk.1_Silent_p.V419V	NM_006162	NP_006153	O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytosolic	432	RHD.				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)														---	---	---	---
THEG	51298	broad.mit.edu	37	19	371216	371216	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:371216G>A	uc002lol.2	-	6	781	c.742C>T	c.(742-744)CCC>TCC	p.P248S	THEG_uc002lom.2_Missense_Mutation_p.P224S	NM_016585	NP_057669	Q9P2T0	THEG_HUMAN	Theg homolog isoform 1	248					cell differentiation|chaperone-mediated protein complex assembly|multicellular organismal development|spermatogenesis	nucleus	protein binding			ovary(1)	1		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
ABCA7	10347	broad.mit.edu	37	19	1058883	1058883	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1058883C>T	uc002lqw.3	+	39	5575	c.5344C>T	c.(5344-5346)CGG>TGG	p.R1782W	ABCA7_uc002lqy.2_Missense_Mutation_p.R235W|ABCA7_uc010dsc.2_RNA	NM_019112	NP_061985	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A, member 7	1782					phagocytosis|transmembrane transport	ATP-binding cassette (ABC) transporter complex|endosome membrane|Golgi membrane|integral to membrane|plasma membrane	ATP binding|ATPase activity|transporter activity			pancreas(7)|ovary(1)|central_nervous_system(1)	9		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
MUM1	84939	broad.mit.edu	37	19	1366373	1366373	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1366373A>C	uc010xgm.1	+	7	1423	c.1354A>C	c.(1354-1356)ATG>CTG	p.M452L	MUM1_uc010dsi.2_Missense_Mutation_p.M384L|MUM1_uc002lrz.2_Missense_Mutation_p.M453L|MUM1_uc002lsb.2_Missense_Mutation_p.M384L			Q2TAK8	MUM1_HUMAN	SubName: Full=MUM1 protein;	452	PWWP.				chromatin organization|DNA repair	nucleus	nucleosome binding|protein binding				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
ZNF77	58492	broad.mit.edu	37	19	2934734	2934734	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2934734C>T	uc002lws.3	-	4	522	c.391G>A	c.(391-393)GTG>ATG	p.V131M		NM_021217	NP_067040	Q15935	ZNF77_HUMAN	zinc finger protein 77	131					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|zinc ion binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|GBM - Glioblastoma multiforme(1328;2.11e-07)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.174)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
EEF2	1938	broad.mit.edu	37	19	3977228	3977228	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3977228C>T	uc002lze.2	-	14	2451	c.2368G>A	c.(2368-2370)GTC>ATC	p.V790I		NM_001961	NP_001952	P13639	EF2_HUMAN	eukaryotic translation elongation factor 2	790						cytosol|ribonucleoprotein complex	GTP binding|GTPase activity|protein binding|translation elongation factor activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|GBM - Glioblastoma multiforme(1328;0.0223)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
ARRDC5	645432	broad.mit.edu	37	19	4891487	4891487	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4891487C>T	uc002mbm.2	-	3	600	c.600G>A	c.(598-600)ACG>ACA	p.T200T		NM_001080523	NP_001073992	A6NEK1	ARRD5_HUMAN	arrestin domain containing 5	200					signal transduction						0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0257)														---	---	---	---
ZNRF4	148066	broad.mit.edu	37	19	5456087	5456087	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5456087C>T	uc002mca.3	+	1	662	c.585C>T	c.(583-585)AGC>AGT	p.S195S		NM_181710	NP_859061	Q8WWF5	ZNRF4_HUMAN	zinc and ring finger 4 precursor	195	Extracellular (Potential).|PA.					integral to membrane	zinc ion binding			large_intestine(2)	2				UCEC - Uterine corpus endometrioid carcinoma (162;0.0002)														---	---	---	---
ACSBG2	81616	broad.mit.edu	37	19	6147647	6147647	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6147647C>T	uc002mef.1	+	3	485	c.258C>T	c.(256-258)TAC>TAT	p.Y86Y	ACSBG2_uc002mee.1_5'UTR|ACSBG2_uc002meg.1_Silent_p.Y86Y|ACSBG2_uc002meh.1_Silent_p.Y86Y|ACSBG2_uc002mei.1_Silent_p.Y36Y|ACSBG2_uc010xiz.1_Silent_p.Y86Y	NM_030924	NP_112186	Q5FVE4	ACBG2_HUMAN	bubblegum-related acyl-CoA synthetase 2	86					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																		---	---	---	---
PNPLA6	10908	broad.mit.edu	37	19	7621405	7621405	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7621405T>C	uc010xjq.1	+	27	3385	c.3190T>C	c.(3190-3192)TCT>CCT	p.S1064P	PNPLA6_uc002mgq.1_Missense_Mutation_p.S1016P|PNPLA6_uc010xjp.1_Missense_Mutation_p.S989P|PNPLA6_uc002mgr.1_Missense_Mutation_p.S1016P|PNPLA6_uc002mgs.2_Missense_Mutation_p.S1054P|PNPLA6_uc002mgt.1_RNA	NM_006702	NP_006693	Q8IY17	PLPL6_HUMAN	neuropathy target esterase isoform b	1055	Patatin.|Cytoplasmic (Potential).				cell death|lipid catabolic process|phosphatidylcholine metabolic process	endoplasmic reticulum membrane|integral to membrane	lysophospholipase activity			ovary(3)	3																		---	---	---	---
STXBP2	6813	broad.mit.edu	37	19	7706923	7706923	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7706923C>T	uc002mha.3	+	8	627	c.582C>T	c.(580-582)GGC>GGT	p.G194G	STXBP2_uc002mhb.3_Silent_p.G191G|STXBP2_uc010dvj.2_RNA|STXBP2_uc010xjr.1_Silent_p.G205G|STXBP2_uc010dvk.2_Silent_p.G162G|STXBP2_uc002mhc.3_5'UTR|STXBP2_uc002mhe.1_5'Flank	NM_006949	NP_008880	Q15833	STXB2_HUMAN	syntaxin binding protein 2 isoform a	194					leukocyte mediated cytotoxicity|neutrophil degranulation|protein transport|regulation of mast cell degranulation|vesicle docking involved in exocytosis	azurophil granule|cytolytic granule|cytosol|specific granule|tertiary granule	syntaxin-3 binding			central_nervous_system(1)	1																		---	---	---	---
MUC16	94025	broad.mit.edu	37	19	9057368	9057368	+	Silent	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9057368G>T	uc002mkp.2	-	3	30282	c.30078C>A	c.(30076-30078)TCC>TCA	p.S10026S		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	10028	Ser-rich.|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																		---	---	---	---
MUC16	94025	broad.mit.edu	37	19	9062379	9062379	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9062379A>G	uc002mkp.2	-	3	25271	c.25067T>C	c.(25066-25068)GTG>GCG	p.V8356A		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	8358	Ser-rich.|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																		---	---	---	---
MUC16	94025	broad.mit.edu	37	19	9073054	9073054	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9073054T>C	uc002mkp.2	-	3	14596	c.14392A>G	c.(14392-14394)ACC>GCC	p.T4798A		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	4800	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																		---	---	---	---
MUC16	94025	broad.mit.edu	37	19	9075311	9075311	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9075311C>A	uc002mkp.2	-	3	12339	c.12135G>T	c.(12133-12135)AAG>AAT	p.K4045N		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	4047	Thr-rich.|Extracellular (Potential).|Ser-rich.				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	9091740	9091740	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9091740T>G	uc002mkp.2	-	1	279	c.75A>C	c.(73-75)AAA>AAC	p.K25N		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	25	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																		---	---	---	---
PDE4A	5141	broad.mit.edu	37	19	10563963	10563963	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10563963C>T	uc002moj.2	+						PDE4A_uc002mok.2_Intron|PDE4A_uc002mol.2_Intron|PDE4A_uc002mom.2_Silent_p.C8C|PDE4A_uc002mon.2_5'UTR	NM_001111307	NP_001104777			phosphodiesterase 4A isoform 1						signal transduction	cytosol|membrane fraction|perinuclear region of cytoplasm|ruffle membrane|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(20;5.8e-10)|Epithelial(33;7.58e-07)|all cancers(31;3.91e-06)		Cilostazol(DB01166)|Dipyridamole(DB00975)|Dyphylline(DB00651)|Enprofylline(DB00824)|Iloprost(DB01088)|Milrinone(DB00235)|Pentoxifylline(DB00806)|Phentolamine(DB00692)|Tadalafil(DB00820)|Theophylline(DB00277)													---	---	---	---
AP1M2	10053	broad.mit.edu	37	19	10690477	10690477	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10690477A>C	uc002mpc.2	-	7	815	c.731T>G	c.(730-732)CTC>CGC	p.L244R	AP1M2_uc002mpd.2_Missense_Mutation_p.L246R	NM_005498	NP_005489	Q9Y6Q5	AP1M2_HUMAN	adaptor-related protein complex 1, mu 2 subunit	244	MHD.				cellular membrane organization|post-Golgi vesicle-mediated transport|protein targeting|regulation of defense response to virus by virus|vesicle targeting|viral reproduction	clathrin adaptor complex|clathrin coated vesicle membrane|cytosol|Golgi membrane|lysosomal membrane	protein binding			ovary(2)	2			Epithelial(33;1.58e-05)|all cancers(31;6.36e-05)															---	---	---	---
KANK2	25959	broad.mit.edu	37	19	11289124	11289124	+	Splice_Site	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11289124C>A	uc010dxv.2	-	8	1976	c.1418_splice	c.e8-1	p.G473_splice	KANK2_uc002mqm.2_Missense_Mutation_p.G481C|KANK2_uc002mqo.3_Splice_Site_p.G473_splice|KANK2_uc002mqp.1_Splice_Site_p.G282_splice	NM_015493	NP_056308			ankyrin repeat domain 25 isoform 1												0																		---	---	---	---
DOCK6	57572	broad.mit.edu	37	19	11323972	11323972	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11323972C>A	uc002mqs.3	-	35	4412	c.4371G>T	c.(4369-4371)GAG>GAT	p.E1457D	DOCK6_uc010xlq.1_Missense_Mutation_p.E796D	NM_020812	NP_065863	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	1457					blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(2)|skin(1)	3																		---	---	---	---
CCDC151	115948	broad.mit.edu	37	19	11541519	11541519	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11541519C>A	uc002mrs.2	-	3	587	c.444G>T	c.(442-444)CAG>CAT	p.Q148H	CCDC151_uc002mrr.2_Missense_Mutation_p.Q83H|CCDC151_uc010dxz.2_Intron	NM_145045	NP_659482	A5D8V7	CC151_HUMAN	coiled-coil domain containing 151	148	Potential.									ovary(1)	1																		---	---	---	---
ZNF833	401898	broad.mit.edu	37	19	11796077	11796077	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11796077T>C	uc010dyg.2	+	3	698	c.36T>C	c.(34-36)TGT>TGC	p.C12C	ZNF833_uc002msl.3_RNA	NM_001013691	NP_001013713			zinc finger protein 833												0																		---	---	---	---
ZNF439	90594	broad.mit.edu	37	19	11978419	11978419	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11978419G>T	uc002mss.2	+	3	663	c.535G>T	c.(535-537)GAT>TAT	p.D179Y	ZNF439_uc002msr.2_Missense_Mutation_p.D43Y	NM_152262	NP_689475	Q8NDP4	ZN439_HUMAN	zinc finger protein 439	179					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1																		---	---	---	---
ZNF763	284390	broad.mit.edu	37	19	12089789	12089789	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12089789G>A	uc002msw.2	+	4	1205	c.1050G>A	c.(1048-1050)ACG>ACA	p.T350T	ZNF763_uc010xmf.1_Silent_p.T370T|ZNF763_uc002msv.2_Silent_p.T353T|ZNF763_uc010xmg.1_Silent_p.T228T	NM_001012753	NP_001012771	Q0D2J5	ZN763_HUMAN	zinc finger protein 763	350	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
ZNF709	163051	broad.mit.edu	37	19	12638734	12638734	+	Intron	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12638734G>A	uc002mtx.3	-						ZNF564_uc002mty.2_Intron	NM_001145647	NP_001139119			zinc finger protein 709 isoform b						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF490	57474	broad.mit.edu	37	19	12691704	12691704	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12691704A>C	uc002mtz.2	-	5	1314	c.1185T>G	c.(1183-1185)TGT>TGG	p.C395W		NM_020714	NP_065765	Q9ULM2	ZN490_HUMAN	zinc finger protein 490	395	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
TNPO2	30000	broad.mit.edu	37	19	12829981	12829981	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12829981G>A	uc002muo.2	-	4	372	c.187C>T	c.(187-189)CGC>TGC	p.R63C	TNPO2_uc002mup.2_Missense_Mutation_p.R155C|TNPO2_uc002muq.2_Missense_Mutation_p.R63C|TNPO2_uc002mur.2_Missense_Mutation_p.R63C	NM_001136196	NP_001129668	O14787	TNPO2_HUMAN	transportin 2 (importin 3, karyopherin beta 2b)	63	Importin N-terminal.				intracellular protein transport	cytoplasm|nucleus	nuclear localization sequence binding|protein binding|protein transporter activity			ovary(1)	1																		---	---	---	---
CACNA1A	773	broad.mit.edu	37	19	13476279	13476279	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13476279T>C	uc010dze.2	-	5	872	c.636A>G	c.(634-636)TTA>TTG	p.L212L	CACNA1A_uc002mwy.3_Silent_p.L212L	NM_001127221	NP_001120693	O00555	CAC1A_HUMAN	calcium channel, alpha 1A subunit isoform 3	212	Cytoplasmic (Potential).|I.				cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding			large_intestine(2)	2			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)													---	---	---	---
RLN3	117579	broad.mit.edu	37	19	14141563	14141563	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14141563G>A	uc002mxw.1	+	2	232	c.232G>A	c.(232-234)GCA>ACA	p.A78T	IL27RA_uc002mxx.2_5'Flank|RLN3_uc010dzj.1_3'UTR	NM_080864	NP_543140	Q8WXF3	REL3_HUMAN	relaxin 3 preproprotein	78						extracellular region	hormone activity				0																		---	---	---	---
ZNF333	84449	broad.mit.edu	37	19	14829633	14829633	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14829633A>G	uc002mzn.2	+	12	1628	c.1494A>G	c.(1492-1494)CGA>CGG	p.R498R	ZNF333_uc002mzk.3_Silent_p.R389R	NM_032433	NP_115809	Q96JL9	ZN333_HUMAN	zinc finger protein 333	498	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
ILVBL	10994	broad.mit.edu	37	19	15230320	15230320	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15230320G>A	uc002nam.2	-	8	944	c.823C>T	c.(823-825)CGC>TGC	p.R275C	ILVBL_uc010xof.1_5'Flank|ILVBL_uc010dzw.2_Missense_Mutation_p.R168C	NM_006844	NP_006835	A1L0T0	ILVBL_HUMAN	ilvB (bacterial acetolactate synthase)-like	275						integral to membrane	magnesium ion binding|thiamine pyrophosphate binding|transferase activity			ovary(2)	2																		---	---	---	---
CYP4F8	11283	broad.mit.edu	37	19	15739144	15739144	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15739144T>C	uc002nbi.2	+	12	1212	c.1148T>C	c.(1147-1149)ATG>ACG	p.M383T	CYP4F8_uc010xoj.1_Missense_Mutation_p.M195T	NM_007253	NP_009184	P98187	CP4F8_HUMAN	cytochrome P450, family 4, subfamily F,	383					prostaglandin metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	alkane 1-monooxygenase activity|aromatase activity|electron carrier activity|heme binding|oxygen binding|protein binding			large_intestine(1)	1																		---	---	---	---
OR10H1	26539	broad.mit.edu	37	19	15918008	15918008	+	Silent	SNP	C	T	T	rs61745312	byFrequency;by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15918008C>T	uc002nbq.2	-	1	929	c.840G>A	c.(838-840)ACG>ACA	p.T280T		NM_013940	NP_039228	Q9Y4A9	O10H1_HUMAN	olfactory receptor, family 10, subfamily H,	280	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0																		---	---	---	---
HSH2D	84941	broad.mit.edu	37	19	16268097	16268097	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16268097G>T	uc002ndp.3	+	8	1083	c.552G>T	c.(550-552)AAG>AAT	p.K184N	HSH2D_uc002ndr.2_Missense_Mutation_p.K127N|HSH2D_uc010ead.2_RNA	NM_032855	NP_116244	Q96JZ2	HSH2D_HUMAN	hematopoietic SH2 domain containing	184						cytoplasm|nucleus					0																		---	---	---	---
EPS15L1	58513	broad.mit.edu	37	19	16551665	16551665	+	Intron	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16551665G>A	uc002ndz.1	-						EPS15L1_uc002ndx.2_Intron|EPS15L1_uc002ndy.2_Intron|EPS15L1_uc010xpf.1_Intron|EPS15L1_uc002nea.1_Intron|EPS15L1_uc010eah.1_Intron|EPS15L1_uc002nec.1_Intron	NM_021235	NP_067058			epidermal growth factor receptor pathway						endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway	coated pit|nucleus|plasma membrane	calcium ion binding			ovary(3)|skin(2)	5																		---	---	---	---
SIN3B	23309	broad.mit.edu	37	19	16952632	16952632	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16952632G>A	uc002ney.1	+	4	449	c.435G>A	c.(433-435)CCG>CCA	p.P145P	SIN3B_uc002new.2_Silent_p.P145P|SIN3B_uc002nex.2_Silent_p.P77P|SIN3B_uc002nez.1_Silent_p.P145P	NM_015260	NP_056075	O75182	SIN3B_HUMAN	SIN3 homolog B, transcription regulator	145					cellular lipid metabolic process|transcription, DNA-dependent	nucleoplasm	protein binding			ovary(2)	2																		---	---	---	---
CPAMD8	27151	broad.mit.edu	37	19	17057979	17057979	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17057979C>T	uc002nfb.2	-	21	2740	c.2708G>A	c.(2707-2709)CGC>CAC	p.R903H		NM_015692	NP_056507	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain	856						extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1)	13																		---	---	---	---
MYO9B	4650	broad.mit.edu	37	19	17311507	17311507	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17311507G>A	uc010eak.2	+	26	4584	c.4432G>A	c.(4432-4434)GGC>AGC	p.G1478S	MYO9B_uc002nfi.2_Missense_Mutation_p.G1478S|MYO9B_uc002nfj.1_Missense_Mutation_p.G1478S|MYO9B_uc002nfl.1_Missense_Mutation_p.G27S	NM_004145	NP_004136	Q13459	MYO9B_HUMAN	myosin IXB isoform 1	1478	Tail.				actin filament-based movement	cell cortex|cytosol|filamentous actin|myosin complex|perinuclear region of cytoplasm	actin binding|ADP binding|ATP binding|ATPase activity|calmodulin binding|metal ion binding|microfilament motor activity|Rho GTPase activator activity			breast(1)	1																		---	---	---	---
USHBP1	83878	broad.mit.edu	37	19	17370820	17370820	+	Silent	SNP	C	T	T	rs142526381		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17370820C>T	uc002nfs.1	-	5	767	c.654G>A	c.(652-654)CTG>CTA	p.L218L	USHBP1_uc002nfr.1_5'Flank|USHBP1_uc002nft.1_RNA|USHBP1_uc010xpk.1_Silent_p.L154L|USHBP1_uc010eam.1_Silent_p.L146L	NM_031941	NP_114147	Q8N6Y0	USBP1_HUMAN	Usher syndrome 1C binding protein 1	218	Potential.						PDZ domain binding			ovary(1)	1																		---	---	---	---
DDA1	79016	broad.mit.edu	37	19	17426810	17426810	+	Intron	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17426810G>A	uc002ngd.2	+						DDA1_uc002nge.2_Intron	NM_024050	NP_076955			DET1 and DDB1 associated 1											ovary(1)	1																		---	---	---	---
GATAD2A	54815	broad.mit.edu	37	19	19576391	19576391	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19576391C>T	uc010xqt.1	+	2	549	c.237C>T	c.(235-237)GGC>GGT	p.G79G	GATAD2A_uc010xqu.1_5'UTR|GATAD2A_uc010xqv.1_Silent_p.G98G|GATAD2A_uc010xqw.1_5'UTR	NM_017660	NP_060130	Q86YP4	P66A_HUMAN	GATA zinc finger domain containing 2A	79					DNA methylation|negative regulation of transcription, DNA-dependent	nuclear speck|NuRD complex	protein binding, bridging|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
GMIP	51291	broad.mit.edu	37	19	19749206	19749206	+	Intron	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19749206C>A	uc002nnd.2	-						GMIP_uc010xrb.1_Intron|GMIP_uc010xrc.1_Intron	NM_016573	NP_057657			GEM interacting protein						negative regulation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	metal ion binding|protein binding|Rho GTPase activator activity			ovary(1)	1																		---	---	---	---
ZNF506	440515	broad.mit.edu	37	19	19916847	19916847	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19916847T>G	uc010eci.2	-	3	367	c.219A>C	c.(217-219)AAA>AAC	p.K73N	ZNF506_uc002nog.2_RNA|ZNF506_uc002noh.3_Intron|ZNF506_uc010ecj.1_RNA	NM_001099269	NP_001092739	Q5JVG8	ZN506_HUMAN	zinc finger protein 506 isoform 1	73	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF253	56242	broad.mit.edu	37	19	20002440	20002440	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20002440T>C	uc002noj.2	+	4	476	c.384T>C	c.(382-384)GGT>GGC	p.G128G	ZNF253_uc002nok.2_Silent_p.G52G|ZNF253_uc002nol.2_RNA	NM_021047	NP_066385	O75346	ZN253_HUMAN	zinc finger protein 253	128					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF253	56242	broad.mit.edu	37	19	20003502	20003502	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20003502G>A	uc002noj.2	+	4	1538	c.1446G>A	c.(1444-1446)GTG>GTA	p.V482V	ZNF253_uc002nok.2_Silent_p.V406V|ZNF253_uc002nol.2_RNA	NM_021047	NP_066385	O75346	ZN253_HUMAN	zinc finger protein 253	482					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF43	7594	broad.mit.edu	37	19	22018849	22018849	+	5'UTR	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22018849T>G	uc002nqj.2	-	1					ZNF43_uc010ecv.2_Intron|ZNF43_uc002nql.2_Intron|ZNF43_uc002nqm.2_Intron|ZNF43_uc002nqk.2_5'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)														---	---	---	---
UQCRFS1	7386	broad.mit.edu	37	19	29698830	29698830	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29698830C>T	uc002nsd.2	-	2	561	c.450G>A	c.(448-450)GCG>GCA	p.A150A		NM_006003	NP_005994	P47985	UCRI_HUMAN	ubiquinol-cytochrome c reductase, Rieske	150					respiratory electron transport chain	integral to membrane|mitochondrial respiratory chain complex III	2 iron, 2 sulfur cluster binding|metal ion binding|ubiquinol-cytochrome-c reductase activity				0	Breast(6;0.0545)|Esophageal squamous(110;0.239)		Lung(7;0.092)															---	---	---	---
ANKRD27	84079	broad.mit.edu	37	19	33118999	33118999	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33118999A>G	uc002ntn.1	-	15	1566	c.1410T>C	c.(1408-1410)GCT>GCC	p.A470A		NM_032139	NP_115515	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	470	ANK 2.				early endosome to late endosome transport	early endosome|lysosome	GTPase activator activity|guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)	5	Esophageal squamous(110;0.137)																	---	---	---	---
CHST8	64377	broad.mit.edu	37	19	34263411	34263411	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34263411G>A	uc002nus.3	+	5	1223	c.718G>A	c.(718-720)GAC>AAC	p.D240N	CHST8_uc002nut.3_Missense_Mutation_p.D240N|CHST8_uc002nuu.2_Missense_Mutation_p.D240N	NM_001127895	NP_001121367	Q9H2A9	CHST8_HUMAN	carbohydrate (N-acetylgalactosamine 4-0)	240	Lumenal (Potential).				carbohydrate biosynthetic process|central nervous system development|hormone biosynthetic process|proteoglycan biosynthetic process|sulfur compound metabolic process	Golgi membrane|integral to membrane	N-acetylgalactosamine 4-O-sulfotransferase activity			skin(2)|large_intestine(1)|ovary(1)	4	Esophageal squamous(110;0.162)																	---	---	---	---
CHST8	64377	broad.mit.edu	37	19	34263835	34263835	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34263835C>T	uc002nus.3	+	5	1647	c.1142C>T	c.(1141-1143)GCG>GTG	p.A381V	CHST8_uc002nut.3_Missense_Mutation_p.A381V|CHST8_uc002nuu.2_Missense_Mutation_p.A381V	NM_001127895	NP_001121367	Q9H2A9	CHST8_HUMAN	carbohydrate (N-acetylgalactosamine 4-0)	381	Lumenal (Potential).				carbohydrate biosynthetic process|central nervous system development|hormone biosynthetic process|proteoglycan biosynthetic process|sulfur compound metabolic process	Golgi membrane|integral to membrane	N-acetylgalactosamine 4-O-sulfotransferase activity			skin(2)|large_intestine(1)|ovary(1)	4	Esophageal squamous(110;0.162)																	---	---	---	---
ATP4A	495	broad.mit.edu	37	19	36047994	36047994	+	Intron	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36047994A>G	uc002oal.1	-						ATP4A_uc010eee.1_Intron	NM_000704	NP_000695			hydrogen/potassium-exchanging ATPase 4A						ATP biosynthetic process|ATP hydrolysis coupled proton transport	integral to plasma membrane	ATP binding|hydrogen:potassium-exchanging ATPase activity|magnesium ion binding			ovary(1)	1	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)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)|Trifluoperazine(DB00831)													---	---	---	---
MLL4	9757	broad.mit.edu	37	19	36216435	36216435	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36216435C>A	uc010eei.2	+	13	3698	c.3698C>A	c.(3697-3699)GCC>GAC	p.A1233D		NM_014727	NP_055542	Q9UMN6	MLL4_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 4	1233	PHD-type 1.				chromatin-mediated maintenance of transcription		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(6)|breast(2)|ovary(1)|kidney(1)|skin(1)	11	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)															---	---	---	---
MLL4	9757	broad.mit.edu	37	19	36221297	36221297	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36221297G>T	uc010eei.2	+	25	5131	c.5131G>T	c.(5131-5133)GAG>TAG	p.E1711*		NM_014727	NP_055542	Q9UMN6	MLL4_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 4	1711					chromatin-mediated maintenance of transcription		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(6)|breast(2)|ovary(1)|kidney(1)|skin(1)	11	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)															---	---	---	---
MLL4	9757	broad.mit.edu	37	19	36227711	36227711	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36227711A>C	uc010eei.2	+	32	7280	c.7280A>C	c.(7279-7281)GAG>GCG	p.E2427A		NM_014727	NP_055542	Q9UMN6	MLL4_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 4	2427	FYR C-terminal.				chromatin-mediated maintenance of transcription		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(6)|breast(2)|ovary(1)|kidney(1)|skin(1)	11	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)															---	---	---	---
LIN37	55957	broad.mit.edu	37	19	36245037	36245037	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36245037G>A	uc002obm.2	+	8	678	c.564G>A	c.(562-564)ATG>ATA	p.M188I	uc002obl.2_5'Flank	NM_019104	NP_061977	Q96GY3	LIN37_HUMAN	lin-37 homolog	188	Pro-rich.						protein binding				0	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)															---	---	---	---
CLIP3	25999	broad.mit.edu	37	19	36510084	36510084	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36510084G>T	uc010eeq.1	-	7	1325	c.1043C>A	c.(1042-1044)CCT>CAT	p.P348H	uc002ocy.2_Intron|CLIP3_uc002ocz.1_Missense_Mutation_p.P348H	NM_015526	NP_056341	Q96DZ5	CLIP3_HUMAN	CAP-GLY domain containing linker protein 3	348	CAP-Gly 1.				chaperone-mediated protein transport|fat cell differentiation|membrane biogenesis|negative regulation of microtubule polymerization|peptidyl-L-cysteine S-palmitoylation|positive regulation of apoptosis|positive regulation of endocytosis|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose transport|positive regulation of protein phosphorylation	early endosome membrane|Golgi stack|membrane raft|microsome|plasma membrane|recycling endosome membrane|trans-Golgi network membrane	ganglioside binding|microtubule binding			ovary(2)|pancreas(1)|skin(1)	4	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)															---	---	---	---
WDR62	284403	broad.mit.edu	37	19	36557299	36557299	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36557299T>C	uc002odc.2	+	5	622	c.531T>C	c.(529-531)CAT>CAC	p.H177H	WDR62_uc002odd.2_Silent_p.H177H|WDR62_uc002odb.2_Silent_p.H177H	NM_173636	NP_775907	O43379	WDR62_HUMAN	WD repeat domain 62 isoform 2	177	WD 2.				cerebral cortex development	nucleus					0	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)															---	---	---	---
TBCB	1155	broad.mit.edu	37	19	36611713	36611713	+	Intron	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36611713G>T	uc002odg.1	+						TBCB_uc002odh.1_Intron	NM_001281	NP_001272			cytoskeleton associated protein 1						'de novo' posttranslational protein folding|cell differentiation|nervous system development	cytoplasm|microtubule	protein binding				0	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)															---	---	---	---
SIPA1L3	23094	broad.mit.edu	37	19	38682888	38682888	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38682888G>T	uc002ohk.2	+	17	5043	c.4534G>T	c.(4534-4536)GAT>TAT	p.D1512Y		NM_015073	NP_055888	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like	1512					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)															---	---	---	---
LGALS4	3960	broad.mit.edu	37	19	39299406	39299406	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39299406A>G	uc002ojg.2	-	3	531	c.317T>C	c.(316-318)ATA>ACA	p.I106T	LGALS4_uc010xuj.1_Missense_Mutation_p.I106T	NM_006149	NP_006140	P56470	LEG4_HUMAN	galectin-4	106	Galectin 1.				cell adhesion	cytosol|plasma membrane	sugar binding			ovary(1)|skin(1)	2	all_cancers(60;1.02e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)															---	---	---	---
FCGBP	8857	broad.mit.edu	37	19	40368707	40368707	+	Missense_Mutation	SNP	C	T	T	rs144631134	byFrequency	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40368707C>T	uc002omp.3	-	28	12649	c.12641G>A	c.(12640-12642)TGC>TAC	p.C4214Y		NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein precursor	4214	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	41021270	41021270	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41021270G>A	uc002ony.2	+	15	2904	c.2818G>A	c.(2818-2820)GTG>ATG	p.V940M	SPTBN4_uc002onx.2_Missense_Mutation_p.V940M|SPTBN4_uc002onz.2_Missense_Mutation_p.V940M|SPTBN4_uc010egx.2_Translation_Start_Site	NM_020971	NP_066022	Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4 isoform	940	Spectrin 7.				actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(1)|skin(1)	5			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)															---	---	---	---
SNRPA	6626	broad.mit.edu	37	19	41263225	41263225	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41263225C>T	uc002ooz.2	+						SNRPA_uc002opa.2_5'UTR	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)															---	---	---	---
CIC	23152	broad.mit.edu	37	19	42795603	42795603	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42795603G>A	uc002otf.1	+	10	2723	c.2683G>A	c.(2683-2685)GCC>ACC	p.A895T		NM_015125	NP_055940	Q96RK0	CIC_HUMAN	capicua homolog	895	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								---	---	---	---
PSG1	5669	broad.mit.edu	37	19	43372414	43372414	+	Missense_Mutation	SNP	G	A	A	rs138545353	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43372414G>A	uc002ovb.2	-	5	1220	c.1082C>T	c.(1081-1083)CCG>CTG	p.P361L	PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Intron|PSG11_uc002ouw.2_Intron|PSG7_uc002ous.1_Intron|PSG7_uc002out.1_Intron|PSG10_uc002ouv.1_Intron|PSG1_uc002oun.2_Intron|PSG1_uc002our.1_Missense_Mutation_p.P361L|PSG1_uc010eio.1_Missense_Mutation_p.P361L|PSG1_uc002oux.1_Missense_Mutation_p.P290L|PSG1_uc002ouy.1_Missense_Mutation_p.P268L|PSG1_uc002ouz.1_Missense_Mutation_p.P361L|PSG1_uc002ova.1_Missense_Mutation_p.P268L|PSG1_uc002ovc.2_Missense_Mutation_p.P268L|PSG1_uc002ovd.1_Missense_Mutation_p.P361L	NM_006905	NP_008836	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	361	Ig-like C2-type 3.				female pregnancy	extracellular region				ovary(2)	2		Prostate(69;0.00682)																---	---	---	---
CBLC	23624	broad.mit.edu	37	19	45284242	45284242	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45284242G>A	uc002ozs.2	+	2	497	c.434G>A	c.(433-435)TGT>TAT	p.C145Y	CBLC_uc010ejt.2_Missense_Mutation_p.C145Y	NM_012116	NP_036248	Q9ULV8	CBLC_HUMAN	Cas-Br-M (murine) ecotropic retroviral	145	4H.|Cbl-PTB.				cell surface receptor linked signaling pathway|negative regulation of epidermal growth factor receptor activity|negative regulation of MAP kinase activity|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	calcium ion binding|epidermal growth factor receptor binding|phosphotyrosine binding|SH3 domain binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(1)|skin(1)	6	Lung NSC(12;0.00136)|all_lung(12;0.00371)	Ovarian(192;0.231)						M		AML								---	---	---	---
CLPTM1	1209	broad.mit.edu	37	19	45493831	45493831	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45493831C>T	uc002pai.2	+	10	1326	c.1311C>T	c.(1309-1311)GTC>GTT	p.V437V	CLPTM1_uc010xxf.1_Silent_p.V335V|CLPTM1_uc010xxg.1_Silent_p.V423V	NM_001294	NP_001285	O96005	CLPT1_HUMAN	cleft lip and palate associated transmembrane	437	Helical; (Potential).				cell differentiation|multicellular organismal development|regulation of T cell differentiation in thymus	external side of plasma membrane|integral to plasma membrane				ovary(1)	1		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00354)|Epithelial(262;0.187)														---	---	---	---
SIX5	147912	broad.mit.edu	37	19	46269065	46269065	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46269065A>G	uc002pdb.2	-	3	2309	c.1914T>C	c.(1912-1914)CCT>CCC	p.P638P	SIX5_uc002pdc.2_3'UTR	NM_175875	NP_787071	Q8N196	SIX5_HUMAN	SIX homeobox 5	638						cytoplasm|nucleus	protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00783)|GBM - Glioblastoma multiforme(486;0.0802)|Epithelial(262;0.235)														---	---	---	---
FOXA3	3171	broad.mit.edu	37	19	46375801	46375801	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46375801C>A	uc002pdr.2	+	2	735	c.538C>A	c.(538-540)CGT>AGT	p.R180S		NM_004497	NP_004488	P55318	FOXA3_HUMAN	forkhead box A3	180	Fork-head.				brain development|cellular glucose homeostasis|cellular response to starvation|chromatin modification|embryo development|endocrine pancreas development|negative regulation of cell proliferation|neural plate anterior/posterior regionalization|neuron fate specification|positive regulation of hepatocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|spermatogenesis	transcription factor complex	DNA bending activity|double-stranded DNA binding|protein domain specific binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|transcription regulatory region DNA binding			breast(1)	1		Ovarian(192;0.0308)|all_neural(266;0.0476)		OV - Ovarian serous cystadenocarcinoma(262;0.00453)|GBM - Glioblastoma multiforme(486;0.0518)|Epithelial(262;0.236)														---	---	---	---
CABP5	56344	broad.mit.edu	37	19	48543979	48543979	+	Missense_Mutation	SNP	C	T	T	rs144594130		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48543979C>T	uc002phu.1	-	3	246	c.121G>A	c.(121-123)GAT>AAT	p.D41N		NM_019855	NP_062829	Q9NP86	CABP5_HUMAN	calcium binding protein 5	41	EF-hand 1.|1 (Potential).				signal transduction	cytoplasm	calcium ion binding			skin(1)	1		all_cancers(25;1.86e-08)|all_lung(116;1.14e-06)|all_epithelial(76;1.16e-06)|Lung NSC(112;2.54e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;4.09e-05)|all cancers(93;0.000322)|Epithelial(262;0.01)|GBM - Glioblastoma multiforme(486;0.058)														---	---	---	---
LIG1	3978	broad.mit.edu	37	19	48665566	48665566	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48665566A>G	uc002pia.1	-	3	180	c.60T>C	c.(58-60)CCT>CCC	p.P20P	LIG1_uc002phz.1_RNA|LIG1_uc002pib.1_RNA|LIG1_uc010xzf.1_Silent_p.P20P|LIG1_uc010xzg.1_Intron|LIG1_uc010xzh.1_RNA	NM_000234	NP_000225	P18858	DNLI1_HUMAN	DNA ligase I	20					anatomical structure morphogenesis|base-excision repair|cell division|DNA ligation involved in DNA repair|DNA strand elongation involved in DNA replication|double-strand break repair via homologous recombination|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	ATP binding|DNA binding|DNA ligase (ATP) activity|metal ion binding			large_intestine(2)|lung(1)	3		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)								NER					---	---	---	---
MAMSTR	284358	broad.mit.edu	37	19	49217152	49217152	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49217152C>T	uc002pkg.2	-	8	936	c.874G>A	c.(874-876)GAG>AAG	p.E292K	MAMSTR_uc002pkf.2_Missense_Mutation_p.E189K	NM_001130915	NP_001124387	Q6ZN01	MASTR_HUMAN	MEF2 activating motif and SAP domain containing	292	Pro-rich.|Transcription activation (By similarity).				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding			ovary(1)	1																		---	---	---	---
RUVBL2	10856	broad.mit.edu	37	19	49514274	49514274	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49514274A>G	uc002plr.1	+	10	819	c.806A>G	c.(805-807)AAG>AGG	p.K269R	RUVBL2_uc002plq.1_Missense_Mutation_p.K224R|RUVBL2_uc002pls.1_RNA|RUVBL2_uc010emn.1_Missense_Mutation_p.K224R|RUVBL2_uc010yac.1_Missense_Mutation_p.K224R	NM_006666	NP_006657	Q9Y230	RUVB2_HUMAN	RuvB-like 2	269					cellular response to UV|DNA recombination|DNA repair|histone H2A acetylation|histone H4 acetylation|protein folding|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|Ino80 complex|membrane|MLL1 complex|NuA4 histone acetyltransferase complex|nuclear matrix	ATP binding|ATP-dependent DNA helicase activity|damaged DNA binding|identical protein binding|unfolded protein binding				0		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000449)|OV - Ovarian serous cystadenocarcinoma(262;0.000555)|GBM - Glioblastoma multiforme(486;0.00585)|Epithelial(262;0.047)														---	---	---	---
TRPM4	54795	broad.mit.edu	37	19	49713478	49713478	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49713478C>T	uc002pmw.2	+	21	3216	c.3144C>T	c.(3142-3144)GGC>GGT	p.G1048G	TRPM4_uc010emu.2_Silent_p.G903G|TRPM4_uc010yak.1_Silent_p.G512G|TRPM4_uc002pmx.2_Silent_p.G874G|TRPM4_uc010emv.2_Silent_p.G933G|TRPM4_uc010yal.1_Silent_p.G694G|TRPM4_uc002pmy.2_Silent_p.G390G	NM_017636	NP_060106	Q8TD43	TRPM4_HUMAN	transient receptor potential cation channel,	1048	Cytoplasmic (Potential).				dendritic cell chemotaxis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell proliferation|protein sumoylation|regulation of T cell cytokine production	endoplasmic reticulum|Golgi apparatus|integral to membrane|plasma membrane	ATP binding|calcium activated cation channel activity|calmodulin binding			ovary(1)|central_nervous_system(1)	2		all_lung(116;8.54e-05)|Lung NSC(112;0.000139)|all_neural(266;0.0506)|Ovarian(192;0.15)		all cancers(93;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000222)|GBM - Glioblastoma multiforme(486;0.00339)|Epithelial(262;0.00751)														---	---	---	---
C19orf41	126123	broad.mit.edu	37	19	50657947	50657947	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50657947A>G	uc002prp.1	-	6	620	c.533T>C	c.(532-534)ATG>ACG	p.M178T		NM_152358	NP_689571	Q6UXV1	IZUM2_HUMAN	hypothetical protein LOC126123 precursor	178	Extracellular (Potential).					integral to membrane					0		all_neural(266;0.0459)|Ovarian(192;0.0728)		GBM - Glioblastoma multiforme(134;0.00364)|OV - Ovarian serous cystadenocarcinoma(262;0.0052)														---	---	---	---
KLK7	5650	broad.mit.edu	37	19	51480876	51480876	+	Silent	SNP	G	A	A	rs17855561		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51480876G>A	uc002puo.2	-	6	780	c.678C>T	c.(676-678)TGC>TGT	p.C226C	KLK7_uc002pup.2_Silent_p.C226C|KLK7_uc010yco.1_Silent_p.C100C|KLK7_uc010eok.2_Silent_p.C154C	NM_139277	NP_644806	P49862	KLK7_HUMAN	stratum corneum chymotryptic enzyme	226	Peptidase S1.			C -> W (in Ref. 6; AAH32005).	epidermis development|proteolysis	extracellular region	serine-type endopeptidase activity				0		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00382)|GBM - Glioblastoma multiforme(134;0.00895)														---	---	---	---
SIGLEC7	27036	broad.mit.edu	37	19	51645967	51645967	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51645967G>T	uc002pvv.1	+	1	410	c.341G>T	c.(340-342)AGA>ATA	p.R114I	SIGLEC7_uc002pvw.1_Missense_Mutation_p.R114I|SIGLEC7_uc010eoq.1_RNA|SIGLEC7_uc010eor.1_Missense_Mutation_p.R114I	NM_014385	NP_055200	Q9Y286	SIGL7_HUMAN	sialic acid binding Ig-like lectin 7 isoform 1	114	Ig-like V-type.|Extracellular (Potential).				cell adhesion	integral to plasma membrane	receptor activity|sugar binding			large_intestine(1)	1		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000836)|OV - Ovarian serous cystadenocarcinoma(262;0.00297)														---	---	---	---
SIGLEC12	89858	broad.mit.edu	37	19	51995052	51995052	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51995052C>T	uc002pwx.1	-	8	1687	c.1631G>A	c.(1630-1632)AGC>AAC	p.S544N	SIGLEC12_uc002pww.1_Missense_Mutation_p.S426N|SIGLEC12_uc010eoy.1_Missense_Mutation_p.S271N	NM_053003	NP_443729	Q96PQ1	SIG12_HUMAN	sialic acid binding immunoglobulin-like	544	Cytoplasmic (Potential).				cell adhesion	integral to membrane	sugar binding			ovary(3)|skin(2)	5		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)														---	---	---	---
SIGLEC14	100049587	broad.mit.edu	37	19	52147228	52147228	+	Silent	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52147228G>T	uc002pxf.3	-	5	936	c.816C>A	c.(814-816)CTC>CTA	p.L272L		NM_001098612	NP_001092082	Q08ET2	SIG14_HUMAN	sialic acid binding Ig-like lectin 14 precursor	272	Extracellular (Potential).|Ig-like C2-type 2.				cell adhesion	integral to membrane|plasma membrane	protein binding|sugar binding			ovary(1)	1		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000965)|OV - Ovarian serous cystadenocarcinoma(262;0.0195)														---	---	---	---
SIGLEC14	100049587	broad.mit.edu	37	19	52149063	52149063	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52149063C>T	uc002pxf.3	-	3	792	c.672G>A	c.(670-672)ACG>ACA	p.T224T		NM_001098612	NP_001092082	Q08ET2	SIG14_HUMAN	sialic acid binding Ig-like lectin 14 precursor	224	Ig-like C2-type 1.|Extracellular (Potential).				cell adhesion	integral to membrane|plasma membrane	protein binding|sugar binding			ovary(1)	1		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000965)|OV - Ovarian serous cystadenocarcinoma(262;0.0195)														---	---	---	---
ZNF350	59348	broad.mit.edu	37	19	52468326	52468326	+	Silent	SNP	C	T	T	rs146297522		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52468326C>T	uc002pyd.2	-	5	1608	c.1380G>A	c.(1378-1380)GCG>GCA	p.A460A	uc002pyb.2_Intron|uc002pyc.2_Intron	NM_021632	NP_067645	Q9GZX5	ZN350_HUMAN	zinc finger protein 350	460					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)														---	---	---	---
KIR3DX1	90011	broad.mit.edu	37	19	55048284	55048284	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55048284G>A	uc010erm.2	+	1	164	c.152G>A	c.(151-153)CGT>CAT	p.R51H	KIR3DX1_uc010yfa.1_RNA|KIR3DX1_uc010yfb.1_RNA|KIR3DX1_uc010yfc.1_RNA|KIR3DX1_uc010yfd.1_RNA					Homo sapiens killer cell immunoglobulin-like receptor, three domains, X1, mRNA (cDNA clone IMAGE:4849085).											ovary(1)	1				GBM - Glioblastoma multiforme(193;0.099)														---	---	---	---
KIR2DL1	3802	broad.mit.edu	37	19	55286738	55286738	+	Silent	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55286738G>T	uc002qhb.1	+	4	530	c.492G>T	c.(490-492)GGG>GGT	p.G164G	KIR2DS4_uc010yfj.1_Intron|KIR2DS4_uc010yfk.1_Intron|KIR2DL3_uc010erw.1_Intron|KIR2DL1_uc002qgz.1_Intron|KIR2DL3_uc002qha.1_RNA|KIR3DP1_uc010yfi.1_Intron|KIR2DL1_uc010erz.1_Silent_p.G164G	NM_014218	NP_055033	P43626	KI2L1_HUMAN	killer cell immunoglobulin-like receptor, two	164	Extracellular (Potential).|Ig-like C2-type 2.				immune response|natural killer cell inhibitory signaling pathway	integral to plasma membrane	protein binding|receptor activity				0				GBM - Glioblastoma multiforme(193;0.0192)														---	---	---	---
SAPS1	22870	broad.mit.edu	37	19	55750771	55750771	+	Splice_Site	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55750771A>G	uc002qjw.3	-	15	1993	c.1751_splice	c.e15+1	p.N584_splice	SAPS1_uc002qjv.2_Splice_Site_p.N646_splice	NM_014931	NP_055746			SAPS domain family, member 1						regulation of phosphoprotein phosphatase activity	cytoplasm	protein phosphatase binding				0		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0449)														---	---	---	---
U2AF2	11338	broad.mit.edu	37	19	56175047	56175047	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56175047C>T	uc002qlu.2	+	7	1734	c.679C>T	c.(679-681)CGC>TGC	p.R227C	U2AF2_uc002qlt.2_Missense_Mutation_p.R227C	NM_007279	NP_009210	P26368	U2AF2_HUMAN	U2 (RNU2) small nuclear RNA auxiliary factor 2	227	RRM 1.				mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription	nucleoplasm|spliceosomal complex	enzyme binding|nucleotide binding|RNA binding			ovary(1)	1		Colorectal(82;0.00244)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)														---	---	---	---
ZNF582	147948	broad.mit.edu	37	19	56895963	56895963	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56895963G>A	uc002qmz.1	-	5	982	c.823C>T	c.(823-825)CGA>TGA	p.R275*	ZNF582_uc002qmy.2_Nonsense_Mutation_p.R306*	NM_144690	NP_653291	Q96NG8	ZN582_HUMAN	zinc finger protein 582	275	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|large_intestine(1)	4		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0547)														---	---	---	---
ZNF667	63934	broad.mit.edu	37	19	56953357	56953357	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56953357C>A	uc002qnd.2	-	5	1169	c.1007G>T	c.(1006-1008)GGG>GTG	p.G336V	ZNF667_uc010etl.2_Missense_Mutation_p.G118V|ZNF667_uc002qne.2_Missense_Mutation_p.G336V|ZNF667_uc010etm.2_Missense_Mutation_p.G279V	NM_022103	NP_071386	Q5HYK9	ZN667_HUMAN	zinc finger protein 667	336	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)														---	---	---	---
ZNF835	90485	broad.mit.edu	37	19	57176021	57176021	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57176021C>T	uc010ygo.1	-	2	612	c.612G>A	c.(610-612)GCG>GCA	p.A204A	ZNF835_uc010ygn.1_Silent_p.A182A	NM_001005850	NP_001005850			zinc finger protein 835											pancreas(3)|skin(1)	4																		---	---	---	---
ZNF548	147694	broad.mit.edu	37	19	57908483	57908483	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57908483C>T	uc002qom.2	+	2	333	c.83C>T	c.(82-84)GCT>GTT	p.A28V	ZNF547_uc002qpm.3_Intron|ZNF548_uc002qon.2_Missense_Mutation_p.A31V	NM_152909	NP_690873	Q8NEK5	ZN548_HUMAN	zinc finger protein 548	28	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)														---	---	---	---
ZNF134	7693	broad.mit.edu	37	19	58132419	58132419	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58132419C>T	uc002qpn.2	+	3	1031	c.932C>T	c.(931-933)ACT>ATT	p.T311I	ZNF134_uc002qpo.2_Missense_Mutation_p.T138I|ZNF211_uc010yhb.1_5'UTR	NM_003435	NP_003426	P52741	ZN134_HUMAN	zinc finger protein 134	311						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)														---	---	---	---
ZNF587	84914	broad.mit.edu	37	19	58361428	58361428	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58361428C>T	uc002qql.2	+	1	160	c.22C>T	c.(22-24)CGC>TGC	p.R8C	ZNF587_uc002qqb.2_Intron|ZNF587_uc010yhh.1_Intron|ZNF587_uc002qqi.1_Intron|ZNF587_uc002qqj.1_Intron|ZNF814_uc002qqk.2_RNA|ZNF587_uc010yhk.1_Missense_Mutation_p.R8C	NM_032828	NP_116217	Q96SQ5	ZN587_HUMAN	zinc finger protein 587	8					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)														---	---	---	---
ZNF135	7694	broad.mit.edu	37	19	58578417	58578417	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58578417A>G	uc010yhq.1	+	5	697	c.601A>G	c.(601-603)ACA>GCA	p.T201A	ZNF135_uc002qre.2_Missense_Mutation_p.T189A|ZNF135_uc002qrd.1_Missense_Mutation_p.T147A|ZNF135_uc002qrf.2_Missense_Mutation_p.T147A|ZNF135_uc002qrg.2_Missense_Mutation_p.T159A|ZNF135_uc010yhr.1_Missense_Mutation_p.T10A	NM_003436	NP_003427	B4DHH9	B4DHH9_HUMAN	zinc finger protein 135 isoform 2	201					regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0161)														---	---	---	---
ZNF324	25799	broad.mit.edu	37	19	58982407	58982407	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58982407C>T	uc002qsw.1	+	4	642	c.548C>T	c.(547-549)GCG>GTG	p.A183V	ZNF324_uc002qsx.1_5'UTR	NM_014347	NP_055162	O75467	Z324A_HUMAN	zinc finger protein 324	183					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)														---	---	---	---
SLC27A5	10998	broad.mit.edu	37	19	59021339	59021339	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:59021339C>A	uc002qtc.2	-	3	1042	c.932G>T	c.(931-933)CGG>CTG	p.R311L		NM_012254	NP_036386	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid	311	Cytoplasmic (Probable).				bile acid and bile salt transport|bile acid biosynthetic process|very long-chain fatty acid metabolic process	endoplasmic reticulum membrane|integral to membrane	ATP binding|cholate-CoA ligase activity|long-chain fatty acid-CoA ligase activity				0		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.181)														---	---	---	---
TRIM28	10155	broad.mit.edu	37	19	59059042	59059042	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:59059042T>C	uc002qtg.1	+	5	1090	c.801T>C	c.(799-801)CAT>CAC	p.H267H	TRIM28_uc010eut.1_Silent_p.H185H|TRIM28_uc002qth.1_5'Flank	NM_005762	NP_005753	Q13263	TIF1B_HUMAN	tripartite motif-containing 28 protein	267	RBCC domain.|Leucine zipper alpha helical coiled-coil region.				epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent	nucleoplasm	chromo shadow domain binding|ligase activity|transcription corepressor activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)														---	---	---	---
TGM3	7053	broad.mit.edu	37	20	2291713	2291713	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2291713G>A	uc002wfx.3	+	4	575	c.478G>A	c.(478-480)GCC>ACC	p.A160T		NM_003245	NP_003236	Q08188	TGM3_HUMAN	transglutaminase 3 precursor	160					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)													---	---	---	---
CPXM1	56265	broad.mit.edu	37	20	2778856	2778856	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2778856C>T	uc002wgu.2	-	4	596	c.532G>A	c.(532-534)GCT>ACT	p.A178T	CPXM1_uc010gas.2_Missense_Mutation_p.A178T	NM_019609	NP_062555	Q96SM3	CPXM1_HUMAN	carboxypeptidase X, member 1 precursor	178	F5/8 type C.				cell adhesion|proteolysis		metallocarboxypeptidase activity|zinc ion binding			ovary(2)|skin(2)	4																		---	---	---	---
CDC25B	994	broad.mit.edu	37	20	3785242	3785242	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3785242G>A	uc002wjn.2	+	15	2295	c.1517G>A	c.(1516-1518)CGT>CAT	p.R506H	CDC25B_uc010zqk.1_Missense_Mutation_p.R442H|CDC25B_uc010zql.1_Missense_Mutation_p.R428H|CDC25B_uc010zqm.1_Missense_Mutation_p.R415H|CDC25B_uc002wjl.2_Missense_Mutation_p.R394H|CDC25B_uc002wjm.2_Missense_Mutation_p.R394H|CDC25B_uc002wjo.2_Missense_Mutation_p.R492H|CDC25B_uc002wjp.2_Missense_Mutation_p.R465H|CDC25B_uc002wjq.2_Missense_Mutation_p.R306H|CDC25B_uc010gbc.2_Intron	NM_021873	NP_068659	P30305	MPIP2_HUMAN	cell division cycle 25B isoform 1	506	Rhodanese.				cell division|G2/M transition of mitotic cell cycle|mitosis|positive regulation of cell proliferation	cytosol|microtubule organizing center|nucleoplasm	protein binding|protein tyrosine phosphatase activity			lung(3)|ovary(2)	5																		---	---	---	---
SLC23A2	9962	broad.mit.edu	37	20	4850682	4850682	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4850682T>C	uc002wlg.1	-	12	1495	c.1120A>G	c.(1120-1122)ACC>GCC	p.T374A	SLC23A2_uc010zqr.1_Missense_Mutation_p.T259A|SLC23A2_uc002wlh.1_Missense_Mutation_p.T374A|SLC23A2_uc002wli.2_Missense_Mutation_p.T373A	NM_005116	NP_005107	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (nucleobase	374	Helical; (Potential).				L-ascorbic acid metabolic process|molecular hydrogen transport|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|transepithelial L-ascorbic acid transport	apical plasma membrane|integral to plasma membrane|membrane fraction	nucleobase transmembrane transporter activity|sodium-dependent L-ascorbate transmembrane transporter activity|sodium-dependent multivitamin transmembrane transporter activity			ovary(2)	2																		---	---	---	---
PLCB4	5332	broad.mit.edu	37	20	9376197	9376197	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9376197T>C	uc002wnf.2	+	18	1578	c.1442T>C	c.(1441-1443)ATG>ACG	p.M481T	PLCB4_uc010gbw.1_Missense_Mutation_p.M481T|PLCB4_uc010gbx.2_Missense_Mutation_p.M481T|PLCB4_uc002wne.2_Missense_Mutation_p.M481T|PLCB4_uc002wnh.2_Missense_Mutation_p.M328T	NM_182797	NP_877949	Q15147	PLCB4_HUMAN	phospholipase C beta 4 isoform b	481					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																		---	---	---	---
ESF1	51575	broad.mit.edu	37	20	13747501	13747501	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13747501T>G	uc002woj.2	-	8	1697	c.1589A>C	c.(1588-1590)GAG>GCG	p.E530A	ESF1_uc002wok.1_Missense_Mutation_p.E530A	NM_016649	NP_057733	Q9H501	ESF1_HUMAN	ABT1-associated protein	530					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|nucleoplasm				ovary(1)	1																		---	---	---	---
CRNKL1	51340	broad.mit.edu	37	20	20016850	20016850	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20016850T>G	uc002wrs.2	-	15	2568	c.2536A>C	c.(2536-2538)AGT>CGT	p.S846R		NM_016652	NP_057736	Q9BZJ0	CRNL1_HUMAN	crooked neck-like 1 protein	846					spliceosome assembly	catalytic step 2 spliceosome|cytoplasm|nuclear speck	RNA binding			ovary(2)|large_intestine(1)	3																		---	---	---	---
XRN2	22803	broad.mit.edu	37	20	21328808	21328808	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21328808T>C	uc002wsf.1	+	18	1785	c.1690T>C	c.(1690-1692)TAT>CAT	p.Y564H	XRN2_uc002wsg.1_Missense_Mutation_p.Y488H|XRN2_uc010zsk.1_Missense_Mutation_p.Y510H	NM_012255	NP_036387	Q9H0D6	XRN2_HUMAN	5'-3' exoribonuclease 2	564					cell growth|DNA catabolic process, exonucleolytic|mRNA processing|regulation of transcription, DNA-dependent|RNA catabolic process|spermatogenesis|transcription termination, DNA-dependent	nucleolus	5'-3' exoribonuclease activity|nucleic acid binding|protein binding|zinc ion binding			skin(1)	1																		---	---	---	---
KIF3B	9371	broad.mit.edu	37	20	30915396	30915396	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30915396G>T	uc002wxq.2	+	7	2067	c.1900G>T	c.(1900-1902)GGA>TGA	p.G634*	KIF3B_uc010ztw.1_Nonsense_Mutation_p.G572*	NM_004798	NP_004789	O15066	KIF3B_HUMAN	kinesin family member 3B	634	Globular.				anterograde axon cargo transport|blood coagulation|determination of left/right symmetry|mitotic centrosome separation|plus-end-directed vesicle transport along microtubule|spindle assembly involved in mitosis	centrosome|cytosol|kinesin II complex|plus-end kinesin complex|spindle microtubule	ATP binding|plus-end-directed microtubule motor activity|Rho GTPase binding			central_nervous_system(3)|ovary(2)	5			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)															---	---	---	---
C20orf185	359710	broad.mit.edu	37	20	31644484	31644484	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31644484C>T	uc002wym.1	+	2	261	c.261C>T	c.(259-261)GGC>GGT	p.G87G		NM_182658	NP_872599	P59826	LPLC3_HUMAN	antimicrobial peptide RYA3 precursor	87	Leu-rich.				innate immune response	cytoplasm|extracellular region	lipid binding|protein binding			ovary(4)	4																		---	---	---	---
ASIP	434	broad.mit.edu	37	20	32848339	32848339	+	Silent	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32848339G>T	uc002xah.1	+	1	169	c.159G>T	c.(157-159)GTG>GTT	p.V53V		NM_001672	NP_001663	P42127	ASIP_HUMAN	agouti signaling protein precursor	53					cell-cell signaling|generation of precursor metabolites and energy|hormone-mediated signaling pathway	extracellular space				central_nervous_system(1)	1																		---	---	---	---
NCOA6	23054	broad.mit.edu	37	20	33346693	33346693	+	Silent	SNP	C	T	T	rs143078359		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33346693C>T	uc002xav.2	-	7	3129	c.558G>A	c.(556-558)CCG>CCA	p.P186P	NCOA6_uc002xaw.2_Silent_p.P186P|NCOA6_uc010gew.1_Intron	NM_014071	NP_054790	Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	186	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																		---	---	---	---
MYH7B	57644	broad.mit.edu	37	20	33582190	33582190	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33582190C>A	uc002xbi.1	+	25	2904	c.2812C>A	c.(2812-2814)CTG>ATG	p.L938M		NM_020884	NP_065935	A7E2Y1	MYH7B_HUMAN	myosin, heavy polypeptide 7B, cardiac muscle,	896	Potential.					membrane|myosin filament	actin binding|ATP binding|motor activity			ovary(1)|breast(1)	2			BRCA - Breast invasive adenocarcinoma(18;0.00691)															---	---	---	---
MYH7B	57644	broad.mit.edu	37	20	33584234	33584234	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33584234A>G	uc002xbi.1	+	27	3247	c.3155A>G	c.(3154-3156)CAC>CGC	p.H1052R		NM_020884	NP_065935	A7E2Y1	MYH7B_HUMAN	myosin, heavy polypeptide 7B, cardiac muscle,	1010	Potential.					membrane|myosin filament	actin binding|ATP binding|motor activity			ovary(1)|breast(1)	2			BRCA - Breast invasive adenocarcinoma(18;0.00691)															---	---	---	---
DLGAP4	22839	broad.mit.edu	37	20	35125217	35125217	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35125217G>T	uc002xff.2	+	8	2193	c.1758G>T	c.(1756-1758)CAG>CAT	p.Q586H	DLGAP4_uc010zvp.1_Missense_Mutation_p.Q586H|DLGAP4_uc002xfg.2_Translation_Start_Site|DLGAP4_uc002xfh.2_Missense_Mutation_p.Q47H|DLGAP4_uc002xfi.2_Translation_Start_Site|DLGAP4_uc002xfj.2_5'Flank	NM_014902	NP_055717	Q9Y2H0	DLGP4_HUMAN	disks large-associated protein 4 isoform a	586					cell-cell signaling	membrane	protein binding			skin(2)|ovary(1)	3	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)																---	---	---	---
CTNNBL1	56259	broad.mit.edu	37	20	36407655	36407655	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36407655C>A	uc010zvw.1	+	11	1040	c.949C>A	c.(949-951)CTC>ATC	p.L317I	CTNNBL1_uc002xhh.2_Missense_Mutation_p.L130I|CTNNBL1_uc002xhi.2_RNA|CTNNBL1_uc002xhj.2_Missense_Mutation_p.L65I	NM_030877	NP_110517	Q8WYA6	CTBL1_HUMAN	beta catenin-like 1	317					apoptosis|positive regulation of apoptosis|somatic diversification of immunoglobulins	nucleus	enzyme binding			ovary(2)	2		Myeloproliferative disorder(115;0.00878)																---	---	---	---
RALGAPB	57148	broad.mit.edu	37	20	37146531	37146531	+	Silent	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37146531T>G	uc002xiw.2	+	9	1562	c.1305T>G	c.(1303-1305)CCT>CCG	p.P435P	RALGAPB_uc010zvz.1_Silent_p.P435P|RALGAPB_uc002xix.2_Silent_p.P435P|RALGAPB_uc002xiy.1_Silent_p.P435P|RALGAPB_uc002xiz.2_Silent_p.P213P|RALGAPB_uc002xja.1_Silent_p.P162P	NM_020336	NP_065069	Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit	435					activation of Ral GTPase activity	intracellular	protein heterodimerization activity|Ral GTPase activator activity			pancreas(1)|skin(1)	2																		---	---	---	---
CHD6	84181	broad.mit.edu	37	20	40049312	40049312	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40049312G>T	uc002xka.1	-	31	6141	c.5963C>A	c.(5962-5964)CCG>CAG	p.P1988Q		NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1988					chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|skin(5)|lung(2)|central_nervous_system(1)	14		Myeloproliferative disorder(115;0.00425)																---	---	---	---
PTPRT	11122	broad.mit.edu	37	20	40713312	40713312	+	Intron	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40713312T>C	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)																---	---	---	---
GTSF1L	149699	broad.mit.edu	37	20	42355032	42355032	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42355032G>A	uc002xld.2	-	1	611	c.303C>T	c.(301-303)CCC>CCT	p.P101P	GTSF1L_uc002xlc.2_Intron	NM_176791	NP_789761	Q9H1H1	GTSFL_HUMAN	gametocyte specific factor 1-like isoform 1	101							metal ion binding				0		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)															---	---	---	---
PABPC1L	80336	broad.mit.edu	37	20	43564028	43564028	+	Intron	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43564028G>A	uc010ggv.1	+						PABPC1L_uc010zwq.1_Intron|PABPC1L_uc002xmv.2_Intron|PABPC1L_uc002xmw.2_Intron|PABPC1L_uc002xmx.2_Intron	NM_001124756	NP_001118228			poly(A)-binding protein, cytoplasmic 1-like								nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
PIGT	51604	broad.mit.edu	37	20	44047589	44047589	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44047589G>A	uc002xoh.1	+	3	536	c.463G>A	c.(463-465)GCC>ACC	p.A155T	PIGT_uc010ghb.1_Missense_Mutation_p.A145T|PIGT_uc010zwt.1_Intron|PIGT_uc010ghd.1_Silent_p.L95L|PIGT_uc010ghc.1_Intron|PIGT_uc010ghe.1_Intron|PIGT_uc010ghf.1_Silent_p.L141L|PIGT_uc002xoj.1_Missense_Mutation_p.A155T|PIGT_uc002xok.1_Missense_Mutation_p.A155T|PIGT_uc010zwu.1_5'UTR|PIGT_uc002xoi.1_RNA|PIGT_uc010zwv.1_5'UTR|PIGT_uc010zww.1_Intron|PIGT_uc010zwx.1_Silent_p.L23L|PIGT_uc010zwy.1_Intron|PIGT_uc010zwz.1_Intron|PIGT_uc010zxa.1_Intron|PIGT_uc002xol.1_5'UTR|PIGT_uc010zxb.1_5'Flank	NM_015937	NP_057021	Q969N2	PIGT_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	155	Lumenal (Potential).				attachment of GPI anchor to protein|C-terminal protein lipidation	GPI-anchor transamidase complex	protein binding			pancreas(1)	1		Myeloproliferative disorder(115;0.0122)																---	---	---	---
ZNF335	63925	broad.mit.edu	37	20	44582340	44582340	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44582340C>A	uc002xqw.2	-	18	2813	c.2690G>T	c.(2689-2691)GGC>GTC	p.G897V	ZNF335_uc002xqv.2_Missense_Mutation_p.G9V|ZNF335_uc010zxk.1_Missense_Mutation_p.G742V	NM_022095	NP_071378	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	897					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(3)|ovary(1)	4		Myeloproliferative disorder(115;0.0122)																---	---	---	---
CSE1L	1434	broad.mit.edu	37	20	47701884	47701884	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47701884A>G	uc002xty.2	+	16	1818	c.1684A>G	c.(1684-1686)ACA>GCA	p.T562A	CSE1L_uc010zyg.1_Missense_Mutation_p.T345A|CSE1L_uc010ghx.2_Missense_Mutation_p.T506A|CSE1L_uc010ghy.2_Missense_Mutation_p.T183A|CSE1L_uc010zyh.1_Missense_Mutation_p.T211A	NM_001316	NP_001307	P55060	XPO2_HUMAN	CSE1 chromosome segregation 1-like protein	562					apoptosis|cell proliferation|intracellular protein transport	cytoplasm|nucleus	importin-alpha export receptor activity			large_intestine(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(12;0.000491)|Colorectal(8;0.198)															---	---	---	---
SLC9A8	23315	broad.mit.edu	37	20	48431697	48431697	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48431697T>C	uc002xuv.1	+	2	389	c.179T>C	c.(178-180)ATG>ACG	p.M60T	SLC9A8_uc010zym.1_5'UTR|SLC9A8_uc010zyj.1_Missense_Mutation_p.M60T|SLC9A8_uc010zyk.1_Missense_Mutation_p.M60T|SLC9A8_uc010zyl.1_Missense_Mutation_p.M60T|SLC9A8_uc010gib.1_Missense_Mutation_p.M60T	NM_015266	NP_056081	Q9Y2E8	SL9A8_HUMAN	sodium/hydrogen exchanger 8	60	Helical; (Potential).					Golgi membrane|integral to membrane	sodium:hydrogen antiporter activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(9;3.91e-07)															---	---	---	---
RNF114	55905	broad.mit.edu	37	20	48561987	48561987	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48561987T>C	uc002xux.2	+	3	396	c.360T>C	c.(358-360)GGT>GGC	p.G120G	RNF114_uc010zyo.1_Silent_p.G120G|RNF114_uc002xuy.2_RNA	NM_018683	NP_061153	Q9Y508	RN114_HUMAN	zinc finger protein 313	120					cell differentiation|multicellular organismal development|spermatogenesis	intracellular	zinc ion binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
FAM65C	140876	broad.mit.edu	37	20	49236598	49236598	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49236598C>T	uc002xvm.2	-	3	500	c.182G>A	c.(181-183)CGG>CAG	p.R61Q	FAM65C_uc010zyt.1_Missense_Mutation_p.R65Q|FAM65C_uc010zyu.1_RNA|FAM65C_uc002xvn.1_Missense_Mutation_p.R61Q	NM_080829	NP_543019	Q96MK2	FA65C_HUMAN	hypothetical protein LOC140876	61										ovary(2)	2																		---	---	---	---
ZNF217	7764	broad.mit.edu	37	20	52199163	52199163	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52199163A>G	uc002xwq.3	-	1	474	c.203T>C	c.(202-204)ATG>ACG	p.M68T	ZNF217_uc010gij.1_Missense_Mutation_p.M60T	NM_006526	NP_006517	O75362	ZN217_HUMAN	zinc finger protein 217	68	C2H2-type 1.				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)															---	---	---	---
BCAS1	8537	broad.mit.edu	37	20	52601817	52601817	+	Intron	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52601817C>A	uc002xws.2	-						BCAS1_uc010zza.1_Intron|BCAS1_uc010zzb.1_Intron|BCAS1_uc010gim.2_Intron|BCAS1_uc002xwt.2_Intron|BCAS1_uc010gil.1_Intron	NM_003657	NP_003648			breast carcinoma amplified sequence 1							cytoplasm	protein binding			ovary(2)|central_nervous_system(1)	3	Breast(2;9.53e-15)|Lung NSC(4;5.57e-06)|all_lung(4;1.44e-05)		STAD - Stomach adenocarcinoma(23;0.116)|Colorectal(105;0.198)															---	---	---	---
C20orf43	51507	broad.mit.edu	37	20	55052170	55052170	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55052170G>A	uc002xxt.2	+	4	495	c.388G>A	c.(388-390)GGC>AGC	p.G130S	C20orf43_uc010zzf.1_Missense_Mutation_p.G160S|C20orf43_uc002xxu.2_Missense_Mutation_p.G130S|C20orf43_uc002xxv.2_Missense_Mutation_p.G130S	NM_016407	NP_057491	Q9BY42	CT043_HUMAN	hypothetical protein LOC51507	130										ovary(1)	1			Colorectal(105;0.202)															---	---	---	---
C20orf106	200232	broad.mit.edu	37	20	55100912	55100912	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55100912A>G	uc002xxx.2	+	2	382	c.302A>G	c.(301-303)AAA>AGA	p.K101R	GCNT7_uc010zzg.1_5'UTR|C20orf107_uc010zzh.1_Intron	NM_001012971	NP_001012989	Q5JX71	CT106_HUMAN	hypothetical protein LOC200232 precursor	101	Cytoplasmic (Potential).					integral to membrane					0			Colorectal(105;0.202)															---	---	---	---
NPEPL1	79716	broad.mit.edu	37	20	57287611	57287611	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57287611A>G	uc010zzs.1	+	8	1072	c.977A>G	c.(976-978)GAC>GGC	p.D326G	NPEPL1_uc010zzr.1_Missense_Mutation_p.D278G|NPEPL1_uc002xzn.2_RNA|NPEPL1_uc010gjo.1_Missense_Mutation_p.D298G|NPEPL1_uc002xzp.2_Missense_Mutation_p.D214G	NM_024663	NP_078939	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	326					proteolysis	cytoplasm	aminopeptidase activity|manganese ion binding|metalloexopeptidase activity				0	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)															---	---	---	---
CHRNA4	1137	broad.mit.edu	37	20	61981702	61981702	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61981702C>T	uc002yes.2	-	5	1239	c.1061G>A	c.(1060-1062)CGC>CAC	p.R354H	CHRNA4_uc002yet.1_Missense_Mutation_p.R178H|CHRNA4_uc011aaw.1_RNA|CHRNA4_uc010gke.1_Missense_Mutation_p.R283H|CHRNA4_uc002yev.1_Missense_Mutation_p.R178H|CHRNA4_uc010gkf.1_Missense_Mutation_p.R178H	NM_000744	NP_000735	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 subunit	354	Cytoplasmic (Potential).				B cell activation|behavioral response to nicotine|calcium ion transport|cognition|DNA repair|membrane depolarization|regulation of action potential|regulation of dopamine secretion|regulation of inhibitory postsynaptic membrane potential|response to hypoxia|response to oxidative stress|sensory perception of pain|synaptic transmission, cholinergic	cell junction|dendrite|external side of plasma membrane|membrane fraction|neuronal cell body|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity			central_nervous_system(1)|skin(1)	2	all_cancers(38;1.71e-10)				Nicotine(DB00184)|Varenicline(DB01273)													---	---	---	---
KCNQ2	3785	broad.mit.edu	37	20	62038737	62038737	+	Intron	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62038737G>T	uc002yey.1	-						KCNQ2_uc002yez.1_Intron|KCNQ2_uc002yfa.1_Intron|KCNQ2_uc002yfb.1_Intron	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)													---	---	---	---
ZGPAT	84619	broad.mit.edu	37	20	62366861	62366861	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62366861C>T	uc002ygk.2	+	6	1580	c.1402C>T	c.(1402-1404)CGA>TGA	p.R468*	ZGPAT_uc002ygi.2_Nonsense_Mutation_p.R448*|ZGPAT_uc002ygj.2_Nonsense_Mutation_p.R448*|ZGPAT_uc010gkk.1_Nonsense_Mutation_p.R25*|ZGPAT_uc010gkl.1_Nonsense_Mutation_p.R448*|ZGPAT_uc002ygm.2_Nonsense_Mutation_p.R439*|ZGPAT_uc002ygn.3_RNA|LIME1_uc011abi.1_5'Flank|LIME1_uc002ygp.3_5'Flank	NM_032527	NP_115916	Q8N5A5	ZGPAT_HUMAN	zinc finger, CCCH-type with G patch domain	468					negative regulation of epidermal growth factor receptor activity|negative regulation of transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)																	---	---	---	---
MYT1	4661	broad.mit.edu	37	20	62853346	62853346	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62853346T>C	uc002yii.2	+	14	2706	c.2342T>C	c.(2341-2343)CTG>CCG	p.L781P	MYT1_uc002yih.2_Missense_Mutation_p.L483P|MYT1_uc002yij.2_Missense_Mutation_p.L440P	NM_004535	NP_004526	Q01538	MYT1_HUMAN	myelin transcription factor 1	781					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)																	---	---	---	---
TPTE	7179	broad.mit.edu	37	21	10971322	10971322	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10971322C>T	uc002yip.1	-	5	403	c.35G>A	c.(34-36)GGA>GAA	p.G12E	TPTE_uc002yis.1_RNA|TPTE_uc002yiq.1_Missense_Mutation_p.G12E|TPTE_uc002yir.1_Missense_Mutation_p.G12E|TPTE_uc010gkv.1_Intron	NM_199261	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	12					signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)														---	---	---	---
NCAM2	4685	broad.mit.edu	37	21	22910263	22910263	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:22910263C>T	uc002yld.1	+	18	2748	c.2499C>T	c.(2497-2499)GAC>GAT	p.D833D	NCAM2_uc011acb.1_Silent_p.D691D	NM_004540	NP_004531	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2 precursor	833	Cytoplasmic (Potential).				neuron cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)	4		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)														---	---	---	---
KRTAP27-1	643812	broad.mit.edu	37	21	31709612	31709612	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31709612A>G	uc002ynx.1	-	1	401	c.375T>C	c.(373-375)GGT>GGC	p.G125G		NM_001077711	NP_001071179	Q3LI81	KR271_HUMAN	keratin associated protein 27-1	125						intermediate filament				ovary(2)	2																		---	---	---	---
KRTAP13-1	140258	broad.mit.edu	37	21	31768708	31768708	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31768708T>A	uc002yoa.2	+	1	317	c.304T>A	c.(304-306)TTT>ATT	p.F102I		NM_181599	NP_853630	Q8IUC0	KR131_HUMAN	keratin associated protein 13-1	102						intermediate filament				ovary(1)	1																		---	---	---	---
SFRS15	57466	broad.mit.edu	37	21	33044463	33044463	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33044463G>A	uc002ypd.2	-	20	3119	c.2693C>T	c.(2692-2694)GCG>GTG	p.A898V	SFRS15_uc002ype.2_Missense_Mutation_p.A876V|SFRS15_uc010glu.2_Missense_Mutation_p.A883V	NM_020706	NP_065757	O95104	SFR15_HUMAN	splicing factor, arginine/serine-rich 15 isoform	898						nucleus	nucleotide binding|RNA binding				0																		---	---	---	---
C21orf63	59271	broad.mit.edu	37	21	33825719	33825719	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33825719C>T	uc002ypr.1	+	2	670	c.260C>T	c.(259-261)TCG>TTG	p.S87L	C21orf63_uc002ypq.1_Missense_Mutation_p.S87L|C21orf63_uc002yps.1_Intron|C21orf63_uc010glw.1_Missense_Mutation_p.S87L|C21orf63_uc002ypt.1_Intron|C21orf63_uc002ypu.1_5'UTR	NM_058187	NP_478067	P58658	CU063_HUMAN	hypothetical protein LOC59271 precursor	87	SUEL-type lectin 1.|Extracellular (Potential).					integral to membrane	sugar binding			ovary(2)|pancreas(1)	3																OREG0003572	type=REGULATORY REGION|Gene=C21orf63|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
DYRK1A	1859	broad.mit.edu	37	21	38884311	38884311	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38884311A>G	uc002ywk.2	+	11	1844	c.1769A>G	c.(1768-1770)CAT>CGT	p.H590R	DYRK1A_uc002ywi.2_3'UTR|DYRK1A_uc002ywj.2_Missense_Mutation_p.H581R|DYRK1A_uc002ywl.2_3'UTR|DYRK1A_uc002ywm.2_3'UTR|DYRK1A_uc011aei.1_Missense_Mutation_p.H351R	NM_001396	NP_001387	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation	590					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																		---	---	---	---
HMGN1	3150	broad.mit.edu	37	21	40717102	40717102	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40717102A>G	uc002yxo.2	-	5	429	c.225T>C	c.(223-225)CCT>CCC	p.P75P	HMGN1_uc002yxp.2_Missense_Mutation_p.L39P|HMGN1_uc002yxq.2_Missense_Mutation_p.L39P|HMGN1_uc002yxr.2_RNA	NM_004965	NP_004956	P05114	HMGN1_HUMAN	high-mobility group nucleosome binding domain 1	75					positive regulation of transcription elongation, DNA-dependent	chromatin|cytoplasm|nucleus	DNA binding			breast(1)	1		Prostate(19;8.69e-07)																---	---	---	---
LCA5L	150082	broad.mit.edu	37	21	40778192	40778192	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40778192T>C	uc002yxu.2	-	10	1942	c.1629A>G	c.(1627-1629)CCA>CCG	p.P543P	LCA5L_uc002yxv.2_Silent_p.P543P	NM_152505	NP_689718	O95447	LCA5L_HUMAN	Leber congenital amaurosis 5-like	543											0		Prostate(19;1.2e-06)																---	---	---	---
DSCAM	1826	broad.mit.edu	37	21	41457657	41457657	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41457657C>T	uc002yyq.1	-	23	4456	c.4004G>A	c.(4003-4005)CGG>CAG	p.R1335Q	DSCAM_uc002yyr.1_RNA	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform	1335	Extracellular (Potential).|Ig-like C2-type 10.				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)																---	---	---	---
C2CD2	25966	broad.mit.edu	37	21	43309250	43309250	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43309250C>T	uc002yzw.2	-	14	2316	c.2074G>A	c.(2074-2076)GTG>ATG	p.V692M	C2CD2_uc002yzs.2_Missense_Mutation_p.V161M|C2CD2_uc002yzt.2_Missense_Mutation_p.V308M|C2CD2_uc002yzu.2_Missense_Mutation_p.V524M|C2CD2_uc002yzv.2_Missense_Mutation_p.V537M	NM_015500	NP_056315	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2 isoform	692						cytosol|extracellular region|nucleus				ovary(1)	1																		---	---	---	---
TRAPPC10	7109	broad.mit.edu	37	21	45472303	45472303	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45472303G>A	uc002zea.2	+	4	597	c.428G>A	c.(427-429)CGA>CAA	p.R143Q	TRAPPC10_uc010gpo.2_5'UTR|TRAPPC10_uc002zdz.2_Missense_Mutation_p.R143Q	NM_003274	NP_003265	P48553	TPC10_HUMAN	trafficking protein particle complex 10	143					vesicle-mediated transport	Golgi apparatus|integral to membrane	binding|sodium ion transmembrane transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
COL18A1	80781	broad.mit.edu	37	21	46907380	46907380	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46907380G>T	uc011afs.1	+	16	3119	c.3098G>T	c.(3097-3099)GGG>GTG	p.G1033V	COL18A1_uc002zhg.2_Missense_Mutation_p.G618V|COL18A1_uc002zhi.2_Missense_Mutation_p.G798V	NM_130444	NP_569711	P39060	COIA1_HUMAN	alpha 1 type XVIII collagen isoform 3 precursor	1033	Nonhelical region 4 (NC4).				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)														---	---	---	---
GAB4	128954	broad.mit.edu	37	22	17443671	17443671	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17443671C>A	uc002zlw.2	-	10	1785	c.1677G>T	c.(1675-1677)CAG>CAT	p.Q559H		NM_001037814	NP_001032903	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member	559										large_intestine(1)|ovary(1)	2		all_epithelial(15;0.112)|Lung NSC(13;0.248)																---	---	---	---
SLC25A1	6576	broad.mit.edu	37	22	19164451	19164451	+	Missense_Mutation	SNP	G	A	A	rs147446778		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19164451G>A	uc002zoz.2	-	6	654	c.539C>T	c.(538-540)ACG>ATG	p.T180M	SLC25A1_uc002zoy.2_Missense_Mutation_p.T77M|SLC25A1_uc002zpa.2_Missense_Mutation_p.T128M	NM_005984	NP_005975	P53007	TXTP_HUMAN	solute carrier family 25 (mitochondrial carrier;	180	Solcar 2.				gluconeogenesis|long-chain fatty-acyl-CoA biosynthetic process|mitochondrial citrate transport|triglyceride biosynthetic process	integral to membrane|mitochondrial inner membrane	citrate transmembrane transporter activity|protein binding				0	Colorectal(54;0.0993)	all_lung(157;9.94e-09)		Lung(27;0.124)														---	---	---	---
CLTCL1	8218	broad.mit.edu	37	22	19175071	19175071	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19175071T>G	uc002zpb.2	-	30	4679	c.4604A>C	c.(4603-4605)AAG>ACG	p.K1535T	CLTCL1_uc011agv.1_Intron|CLTCL1_uc011agw.1_Missense_Mutation_p.K1514T|CLTCL1_uc011agt.1_Missense_Mutation_p.K326T|CLTCL1_uc011agu.1_Intron	NM_007098	NP_009029	P53675	CLH2_HUMAN	clathrin, heavy polypeptide-like 1 isoform 1	1535	Proximal segment.|Heavy chain arm.				anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network	protein binding|signal transducer activity|structural molecule activity			ovary(4)|central_nervous_system(1)	5	Colorectal(54;0.0993)							T	?	ALCL								---	---	---	---
GNB1L	54584	broad.mit.edu	37	22	19776449	19776449	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19776449A>T	uc002zqe.1	-	7	1161	c.767T>A	c.(766-768)ATC>AAC	p.I256N	GNB1L_uc002zqd.1_Missense_Mutation_p.I112N|GNB1L_uc002zqf.1_Missense_Mutation_p.I256N	NM_053004	NP_443730	Q9BYB4	GNB1L_HUMAN	guanine nucleotide binding protein	256	WD 5.				G-protein coupled receptor protein signaling pathway|intracellular signal transduction	internal side of plasma membrane|intracellular				breast(1)	1	Colorectal(54;0.0993)																	---	---	---	---
DGCR8	54487	broad.mit.edu	37	22	20082241	20082241	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20082241G>A	uc002zri.2	+	9	2061	c.1711G>A	c.(1711-1713)GCT>ACT	p.A571T	DGCR8_uc010grz.2_Missense_Mutation_p.A538T|DGCR8_uc002zrj.2_Missense_Mutation_p.A214T	NM_022720	NP_073557	Q8WYQ5	DGCR8_HUMAN	DiGeorge syndrome critical region gene 8	571	Necessary for interaction with DROSHA.|Necessary for heme-binding and pri-miRNA processing.|DRBM 1.				primary miRNA processing	cytoplasm|cytoplasm|microtubule cytoskeleton|nucleolus|nucleoplasm	double-stranded RNA binding|metal ion binding|protein binding				0	Colorectal(54;0.0993)																	---	---	---	---
KLHL22	84861	broad.mit.edu	37	22	20819376	20819376	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20819376C>T	uc002zsl.1	-	4	990	c.881G>A	c.(880-882)CGG>CAG	p.R294Q	KLHL22_uc011ahr.1_Missense_Mutation_p.R151Q|KLHL22_uc002zsm.1_Missense_Mutation_p.R294Q	NM_032775	NP_116164	Q53GT1	KLH22_HUMAN	kelch-like	294					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)															---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	22516999	22516999	+	Intron	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22516999G>A	uc011aim.1	+						uc011ain.1_RNA					Parts of antibodies, mostly variable regions.												0																		---	---	---	---
RGL4	266747	broad.mit.edu	37	22	24035170	24035170	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24035170A>G	uc002zxn.2	+	3	1858	c.688A>G	c.(688-690)ATG>GTG	p.M230V	LOC91316_uc002zxh.3_RNA|LOC91316_uc002zxi.3_RNA|LOC91316_uc002zxk.3_Intron|LOC91316_uc010gua.2_Intron|LOC91316_uc002zxl.3_Intron|LOC91316_uc011aiz.1_Intron|LOC91316_uc002zxm.3_Intron|RGL4_uc002zxo.2_Missense_Mutation_p.M230V|RGL4_uc002zxp.1_Missense_Mutation_p.M94V|RGL4_uc002zxq.2_Missense_Mutation_p.M94V	NM_153615	NP_705843	Q8IZJ4	RGDSR_HUMAN	ral guanine nucleotide dissociation	230	Ras-GEF.				small GTPase mediated signal transduction	cytoplasmic membrane-bounded vesicle	guanyl-nucleotide exchange factor activity			ovary(1)	1																		---	---	---	---
HPS4	89781	broad.mit.edu	37	22	26860462	26860462	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26860462C>A	uc003acl.2	-	11	1793	c.1134G>T	c.(1132-1134)CAG>CAT	p.Q378H	HPS4_uc003aci.2_Missense_Mutation_p.Q373H|HPS4_uc003acj.2_Missense_Mutation_p.Q242H|HPS4_uc003ack.2_Missense_Mutation_p.Q169H|HPS4_uc003acn.2_Missense_Mutation_p.Q224H|HPS4_uc010gvd.1_Missense_Mutation_p.Q396H|HPS4_uc003ach.2_Missense_Mutation_p.Q113H	NM_022081	NP_071364	Q9NQG7	HPS4_HUMAN	light ear protein isoform a	378					lysosome organization|positive regulation of eye pigmentation|protein stabilization|protein targeting	lysosome|melanosome|membrane fraction|platelet dense granule	protein homodimerization activity				0														Hermansky-Pudlak_syndrome				---	---	---	---
GAS2L1	10634	broad.mit.edu	37	22	29708257	29708257	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29708257G>A	uc003afa.1	+	7	2016	c.1817G>A	c.(1816-1818)AGC>AAC	p.S606N	GAS2L1_uc010gvm.1_Missense_Mutation_p.S379N|GAS2L1_uc003afb.1_3'UTR|GAS2L1_uc003afc.1_Missense_Mutation_p.S606N|GAS2L1_uc003afd.1_3'UTR|GAS2L1_uc003afe.1_3'UTR	NM_152236	NP_689422	Q99501	GA2L1_HUMAN	growth arrest-specific 2 like 1 isoform a	606					cell cycle arrest	cytoplasm|cytoskeleton					0																		---	---	---	---
GATSL3	652968	broad.mit.edu	37	22	30683418	30683418	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30683418C>T	uc003ahd.2	-	3	446	c.316G>A	c.(316-318)GCC>ACC	p.A106T	GATSL3_uc003ahc.2_Missense_Mutation_p.A106T|GATSL3_uc003ahe.2_Missense_Mutation_p.A106T|GATSL3_uc003ahf.2_RNA|GATSL3_uc003ahg.2_RNA|GATSL3_uc003ahh.2_RNA|GATSL3_uc010gvq.2_RNA|GATSL3_uc003ahi.2_Missense_Mutation_p.A279T|GATSL3_uc010gvr.2_5'UTR|GATSL3_uc010gvs.2_5'UTR	NM_001037666	NP_001032755	Q8WTX7	GATL3_HUMAN	GATS protein-like 3	106										breast(1)	1																OREG0026457	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
LIMK2	3985	broad.mit.edu	37	22	31674384	31674384	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31674384C>T	uc003akh.2	+	16	2019	c.1874C>T	c.(1873-1875)ACT>ATT	p.T625I	LIMK2_uc003aki.2_Missense_Mutation_p.T379I|LIMK2_uc003akk.2_Missense_Mutation_p.T604I|LIMK2_uc011aln.1_Missense_Mutation_p.T542I	NM_005569	NP_005560	P53671	LIMK2_HUMAN	LIM domain kinase 2 isoform 2a	625						mitochondrion|nucleus	ATP binding|protein serine/threonine kinase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
SFI1	9814	broad.mit.edu	37	22	32007284	32007284	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32007284A>G	uc003ale.2	+	23	2803	c.2410A>G	c.(2410-2412)AAG>GAG	p.K804E	SFI1_uc003alf.2_Missense_Mutation_p.K773E|SFI1_uc003alg.2_Missense_Mutation_p.K722E|SFI1_uc011alp.1_Missense_Mutation_p.K710E|SFI1_uc011alq.1_Missense_Mutation_p.K749E|SFI1_uc003alh.2_RNA|SFI1_uc010gwi.2_RNA|SFI1_uc003ali.2_5'Flank	NM_001007467	NP_001007468	A8K8P3	SFI1_HUMAN	spindle assembly associated Sfi1 homolog isoform	804					G2/M transition of mitotic cell cycle	centriole|cytosol				central_nervous_system(1)	1																		---	---	---	---
SLC5A4	6527	broad.mit.edu	37	22	32621772	32621772	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32621772C>A	uc003ami.2	-	12	1321	c.1319G>T	c.(1318-1320)TGG>TTG	p.W440L		NM_014227	NP_055042	Q9NY91	SC5A4_HUMAN	solute carrier family 5 (low affinity glucose	440	Helical; (Potential).				carbohydrate transport|sodium ion transport	integral to membrane	symporter activity				0																		---	---	---	---
SYN3	8224	broad.mit.edu	37	22	33265098	33265098	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33265098G>T	uc003amx.2	-	4	635	c.476C>A	c.(475-477)CCA>CAA	p.P159Q	SYN3_uc003amy.2_Missense_Mutation_p.P159Q|SYN3_uc003amz.2_Missense_Mutation_p.P158Q	NM_003490	NP_003481	O14994	SYN3_HUMAN	synapsin III isoform IIIa	159	C; actin-binding and synaptic-vesicle binding.				neurotransmitter secretion	cell junction|synaptic vesicle membrane	ATP binding|ligase activity			skin(1)	1																		---	---	---	---
APOL5	80831	broad.mit.edu	37	22	36122760	36122760	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36122760C>T	uc003aof.2	+	3	645	c.645C>T	c.(643-645)TTC>TTT	p.F215F		NM_030642	NP_085145	Q9BWW9	APOL5_HUMAN	apolipoprotein L5	215					lipid metabolic process|lipid transport|lipoprotein metabolic process	cytoplasm|extracellular region	high-density lipoprotein particle binding|lipid binding|protein binding				0																		---	---	---	---
RBM9	23543	broad.mit.edu	37	22	36164357	36164357	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36164357C>A	uc003aon.3	-	6	815	c.703G>T	c.(703-705)GAC>TAC	p.D235Y	RBM9_uc003aog.3_Missense_Mutation_p.D145Y|RBM9_uc003aol.3_Missense_Mutation_p.D164Y|RBM9_uc003aoj.3_Missense_Mutation_p.D164Y|RBM9_uc003aok.3_Missense_Mutation_p.D165Y|RBM9_uc003aoh.3_Missense_Mutation_p.D164Y|RBM9_uc003aom.3_Missense_Mutation_p.D146Y|RBM9_uc010gwu.2_Missense_Mutation_p.D144Y|RBM9_uc003aoo.3_Missense_Mutation_p.D234Y	NM_001082578	NP_001076047	O43251	RFOX2_HUMAN	RNA binding motif protein 9 isoform 5	174	RRM.				estrogen receptor signaling pathway|mRNA processing|negative regulation of transcription, DNA-dependent|regulation of cell proliferation|RNA splicing	cytoplasm|nucleus	nucleotide binding|RNA binding|transcription corepressor activity|transcription factor binding				0																		---	---	---	---
FOXRED2	80020	broad.mit.edu	37	22	36894042	36894042	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36894042T>C	uc003apn.3	-	5	1486	c.1378A>G	c.(1378-1380)AAG>GAG	p.K460E	FOXRED2_uc003apm.3_Missense_Mutation_p.K12E|FOXRED2_uc003apo.3_Missense_Mutation_p.K460E|FOXRED2_uc003app.3_Missense_Mutation_p.K460E	NM_024955	NP_079231	Q8IWF2	FXRD2_HUMAN	FAD-dependent oxidoreductase domain containing 2	460					ER-associated protein catabolic process	endoplasmic reticulum lumen	flavin adenine dinucleotide binding|oxidoreductase activity|protein binding			lung(1)|kidney(1)	2																		---	---	---	---
KCTD17	79734	broad.mit.edu	37	22	37453491	37453491	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37453491G>A	uc010gxb.2	+	4	466	c.444G>A	c.(442-444)ACG>ACA	p.T148T	KCTD17_uc010gxa.1_Silent_p.T148T|KCTD17_uc011amv.1_Silent_p.T155T|KCTD17_uc010gxc.2_Silent_p.T148T	NM_024681	NP_078957	Q8N5Z5	KCD17_HUMAN	potassium channel tetramerisation domain	155						voltage-gated potassium channel complex	identical protein binding|voltage-gated potassium channel activity				0																		---	---	---	---
ELFN2	114794	broad.mit.edu	37	22	37771287	37771287	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37771287G>A	uc003asq.3	-	3	1074	c.288C>T	c.(286-288)GAC>GAT	p.D96D		NM_052906	NP_443138	Q5R3F8	LRFN6_HUMAN	leucine rich repeat containing 62	96	LRR 2.|Extracellular (Potential).					cell surface|integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	Melanoma(58;0.0574)																	---	---	---	---
MICALL1	85377	broad.mit.edu	37	22	38328644	38328644	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38328644C>A	uc003aui.2	+	11	2185	c.2101C>A	c.(2101-2103)CGT>AGT	p.R701S		NM_033386	NP_203744	Q8N3F8	MILK1_HUMAN	molecule interacting with Rab13	701	Potential.					cytoplasm|cytoskeleton	protein binding|zinc ion binding			breast(1)	1	Melanoma(58;0.045)																	---	---	---	---
NPTXR	23467	broad.mit.edu	37	22	39222651	39222651	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39222651C>T	uc003awk.2	-	3	1106	c.952G>A	c.(952-954)GCA>ACA	p.A318T		NM_014293	NP_055108	O95502	NPTXR_HUMAN	neuronal pentraxin receptor	318	Pentaxin.|Extracellular (Potential).					integral to membrane	metal ion binding			central_nervous_system(2)|skin(1)	3	Melanoma(58;0.04)																	---	---	---	---
APOBEC3B	9582	broad.mit.edu	37	22	39387537	39387537	+	Silent	SNP	C	T	T	rs144471703		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39387537C>T	uc003awo.1	+	6	978	c.924C>T	c.(922-924)TTC>TTT	p.F308F	APOBEC3A_uc011aoc.1_Intron|APOBEC3B_uc003awp.1_Silent_p.F283F|APOBEC3B_uc003awq.1_RNA|APOBEC3D_uc011aod.1_Intron|APOBEC3D_uc011aoe.1_Intron|APOBEC3D_uc011aof.1_Intron	NM_004900	NP_004891	Q9UH17	ABC3B_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic	308					negative regulation of transposition		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines|RNA binding|zinc ion binding			ovary(1)	1	Melanoma(58;0.04)																	---	---	---	---
CACNA1I	8911	broad.mit.edu	37	22	40037069	40037069	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40037069G>A	uc003ayc.2	+	6	938	c.938G>A	c.(937-939)AGC>AAC	p.S313N	CACNA1I_uc003ayd.2_Missense_Mutation_p.S313N|CACNA1I_uc003aye.2_Missense_Mutation_p.S228N|CACNA1I_uc003ayf.2_Missense_Mutation_p.S228N	NM_021096	NP_066919	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type,	313	I.|Extracellular (Potential).				axon guidance|signal transduction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity|protein binding			breast(1)|central_nervous_system(1)	2	Melanoma(58;0.0749)				Flunarizine(DB04841)|Paramethadione(DB00617)|Verapamil(DB00661)													---	---	---	---
L3MBTL2	83746	broad.mit.edu	37	22	41615505	41615505	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41615505G>A	uc003azo.2	+	6	737	c.683G>A	c.(682-684)CGG>CAG	p.R228Q	L3MBTL2_uc010gyi.1_Missense_Mutation_p.R137Q|L3MBTL2_uc003azn.2_RNA|uc003azp.1_5'Flank	NM_031488	NP_113676	Q969R5	LMBL2_HUMAN	l(3)mbt-like 2	228	MBT 1.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	methylated histone residue binding|transcription corepressor activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
RANGAP1	5905	broad.mit.edu	37	22	41650402	41650402	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41650402C>T	uc003azs.2	-	10	2640	c.1170G>A	c.(1168-1170)GAG>GAA	p.E390E	RANGAP1_uc003azt.2_Silent_p.E390E|RANGAP1_uc003azu.2_Silent_p.E390E|RANGAP1_uc003azr.2_5'Flank|RANGAP1_uc010gyk.2_5'Flank|RANGAP1_uc011aoz.1_Silent_p.E335E	NM_002883	NP_002874	P46060	RAGP1_HUMAN	Ran GTPase activating protein 1	390	Asp/Glu-rich (highly acidic).|Asp/Glu-rich (highly acidic).				mitotic prometaphase|signal transduction	condensed chromosome kinetochore|cytosol|nuclear membrane|nuclear pore|soluble fraction|spindle pole	protein binding|Ran GTPase activator activity				0																		---	---	---	---
ZC3H7B	23264	broad.mit.edu	37	22	41735834	41735834	+	Silent	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41735834T>C	uc003azw.2	+	10	1047	c.831T>C	c.(829-831)GGT>GGC	p.G277G	ZC3H7B_uc010gyl.1_Intron	NM_017590	NP_060060	Q9UGR2	Z3H7B_HUMAN	zinc finger CCCH-type containing 7B	293					interspecies interaction between organisms	nucleus	nucleic acid binding|protein binding|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
CCDC134	79879	broad.mit.edu	37	22	42204953	42204953	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42204953C>A	uc003bbh.1	+	2	168	c.59C>A	c.(58-60)GCC>GAC	p.A20D	WBP2NL_uc011ape.1_Intron|LOC339674_uc003bba.1_Intron|CCDC134_uc011apg.1_Missense_Mutation_p.A20D	NM_024821	NP_079097	Q9H6E4	CC134_HUMAN	coiled-coil domain containing 134 precursor	20						extracellular region				ovary(2)	2																		---	---	---	---
EFCAB6	64800	broad.mit.edu	37	22	44004420	44004420	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44004420C>T	uc003bdy.1	-	22	2838	c.2623G>A	c.(2623-2625)GCA>ACA	p.A875T	EFCAB6_uc003bdz.1_Missense_Mutation_p.A723T|EFCAB6_uc010gzi.1_Missense_Mutation_p.A723T|EFCAB6_uc010gzj.1_Intron	NM_022785	NP_073622	Q5THR3	EFCB6_HUMAN	CAP-binding protein complex interacting protein	875	EF-hand 9.				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)																---	---	---	---
LDOC1L	84247	broad.mit.edu	37	22	44892839	44892839	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44892839G>A	uc003beu.1	-	2	935	c.598C>T	c.(598-600)CGA>TGA	p.R200*		NM_032287	NP_115663	Q6ICC9	LDOCL_HUMAN	leucine zipper, down-regulated in cancer 1-like	200										ovary(1)	1		Ovarian(80;0.024)|all_neural(38;0.0416)		LUAD - Lung adenocarcinoma(64;0.0161)														---	---	---	---
PKDREJ	10343	broad.mit.edu	37	22	46654582	46654582	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46654582A>C	uc003bhh.2	-	1	4638	c.4638T>G	c.(4636-4638)GAT>GAG	p.D1546E		NM_006071	NP_006062	Q9NTG1	PKDRE_HUMAN	receptor for egg jelly-like protein precursor	1546	Cytoplasmic (Potential).				acrosome reaction|neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity			breast(3)|ovary(2)	5		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)														---	---	---	---
CELSR1	9620	broad.mit.edu	37	22	46929546	46929546	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46929546C>T	uc003bhw.1	-	1	3522	c.3522G>A	c.(3520-3522)GCG>GCA	p.A1174A		NM_014246	NP_055061	Q9NYQ6	CELR1_HUMAN	cadherin EGF LAG seven-pass G-type receptor 1	1174	Extracellular (Potential).|Cadherin 9.				central nervous system development|homophilic cell adhesion|neural tube closure|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein dimerization activity			lung(4)|breast(4)|pancreas(2)|skin(1)	11		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)														---	---	---	---
MLC1	23209	broad.mit.edu	37	22	50521565	50521565	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50521565A>G	uc003bjg.1	-	3	488	c.215T>C	c.(214-216)CTG>CCG	p.L72P	MLC1_uc011arl.1_Missense_Mutation_p.L72P|MLC1_uc003bjh.1_Missense_Mutation_p.L72P|MLC1_uc011arm.1_Intron|MLC1_uc011arn.1_5'UTR|MLC1_uc011aro.1_Missense_Mutation_p.L72P	NM_139202	NP_631941	Q15049	MLC1_HUMAN	megalencephalic leukoencephalopathy with	72	Helical; (Potential).					basolateral plasma membrane|endosome|integral to membrane|integral to membrane of membrane fraction	ion channel activity			pancreas(1)	1		all_cancers(38;7.69e-11)|all_epithelial(38;9.52e-10)|all_lung(38;3.67e-05)|Breast(42;0.000776)|Lung NSC(38;0.000946)|Ovarian(80;0.0365)|Lung SC(80;0.113)		READ - Rectum adenocarcinoma(2;0.000669)|Colorectal(2;0.00242)|LUAD - Lung adenocarcinoma(64;0.0695)|BRCA - Breast invasive adenocarcinoma(115;0.216)														---	---	---	---
PLXNB2	23654	broad.mit.edu	37	22	50719280	50719280	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50719280C>T	uc003bkv.3	-	24	3992	c.3886G>A	c.(3886-3888)GTG>ATG	p.V1296M	PLXNB2_uc003bkt.1_Missense_Mutation_p.V88M|PLXNB2_uc003bku.1_Missense_Mutation_p.V281M	NM_012401	NP_036533	O15031	PLXB2_HUMAN	plexin B2 precursor	1296	Cytoplasmic (Potential).				regulation of small GTPase mediated signal transduction	integral to membrane|intracellular	GTPase activator activity|protein binding|receptor activity			ovary(4)|central_nervous_system(1)|skin(1)	6		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
CPT1B	1375	broad.mit.edu	37	22	51010460	51010460	+	Missense_Mutation	SNP	C	T	T	rs149756287	by1000genomes	TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:51010460C>T	uc003bmk.3	-	12	1712	c.1550G>A	c.(1549-1551)CGG>CAG	p.R517Q	CPT1B_uc003bml.2_Missense_Mutation_p.R517Q|CPT1B_uc003bmm.2_Missense_Mutation_p.R517Q|CPT1B_uc003bmo.2_Missense_Mutation_p.R517Q|CPT1B_uc011asa.1_Missense_Mutation_p.R483Q|CPT1B_uc003bmn.2_Missense_Mutation_p.R517Q|CPT1B_uc011asb.1_Missense_Mutation_p.R436Q|CHKB-CPT1B_uc003bmp.2_Missense_Mutation_p.R314Q|uc003bmr.1_RNA	NM_001145137	NP_001138609	Q92523	CPT1B_HUMAN	carnitine palmitoyltransferase 1B isoform a	517	Cytoplasmic (Potential).				carnitine shuttle|fatty acid beta-oxidation|regulation of fatty acid oxidation	integral to membrane|mitochondrial outer membrane	carnitine O-palmitoyltransferase activity			ovary(1)|central_nervous_system(1)	2		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		all cancers(3;3.56e-77)|OV - Ovarian serous cystadenocarcinoma(4;5.39e-74)|Epithelial(4;5.58e-70)|GBM - Glioblastoma multiforme(4;5.59e-08)|LUAD - Lung adenocarcinoma(64;0.0016)|Lung(4;0.00942)|BRCA - Breast invasive adenocarcinoma(115;0.207)														---	---	---	---
PLCXD1	55344	broad.mit.edu	37	X	205472	205472	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:205472A>G	uc004cpc.2	+	3	512	c.200A>G	c.(199-201)CAG>CGG	p.Q67R	PLCXD1_uc011mgx.1_RNA	NM_018390	NP_060860	Q9NUJ7	PLCX1_HUMAN	phosphatidylinositol-specific phospholipase C, X	67	PI-PLC X-box.				intracellular signal transduction|lipid metabolic process		phospholipase C activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)																---	---	---	---
SHOX	6473	broad.mit.edu	37	X	595376	595376	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:595376C>T	uc004cph.1	+	3	992	c.301C>T	c.(301-303)CGC>TGC	p.R101C	SHOX_uc004cpi.2_Missense_Mutation_p.R101C	NM_000451	NP_000442	O15266	SHOX_HUMAN	short stature homeobox isoform SHOXa	101					skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)																---	---	---	---
ASMTL	8623	broad.mit.edu	37	X	1546882	1546882	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1546882C>T	uc004cpx.1	-	7	753	c.642G>A	c.(640-642)CCG>CCA	p.P214P	ASMTL_uc011mhe.1_Silent_p.P138P|ASMTL_uc004cpy.1_Silent_p.P198P|ASMTL_uc011mhf.1_Silent_p.P156P	NM_004192	NP_004183	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like	214	MAF-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)																---	---	---	---
P2RY8	286530	broad.mit.edu	37	X	1585207	1585207	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1585207T>C	uc004cpz.2	-	2	493	c.245A>G	c.(244-246)TAC>TGC	p.Y82C		NM_178129	NP_835230	Q86VZ1	P2RY8_HUMAN	G-protein coupled purinergic receptor P2Y8	82	Extracellular (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			lung(5)	5		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)						T	CRLF2	B-ALL|Downs associated ALL								---	---	---	---
MXRA5	25878	broad.mit.edu	37	X	3229337	3229337	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:3229337C>T	uc004crg.3	-	7	7064	c.6907G>A	c.(6907-6909)GTC>ATC	p.V2303I		NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN	adlican precursor	2303	Ig-like C2-type 7.					extracellular region				ovary(5)|lung(1)|central_nervous_system(1)|skin(1)	8		all_lung(23;0.00031)|Lung NSC(23;0.000946)																---	---	---	---
PNPLA4	8228	broad.mit.edu	37	X	7894116	7894116	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7894116G>A	uc011mhq.1	-	2	207	c.45C>T	c.(43-45)GGC>GGT	p.G15G	PNPLA4_uc011mhr.1_Silent_p.G15G|PNPLA4_uc011mhs.1_Intron	NM_004650	NP_004641	P41247	PLPL4_HUMAN	patatin-like phospholipase domain containing 4	15	Patatin.				lipid catabolic process		triglyceride lipase activity				0		Colorectal(8;0.0329)|Medulloblastoma(8;0.232)														OREG0019651	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
FAM9B	171483	broad.mit.edu	37	X	9000448	9000448	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9000448C>A	uc011mhu.1	-	2	172	c.83G>T	c.(82-84)AGG>ATG	p.R28M	FAM9B_uc011mhv.1_RNA|FAM9B_uc004csh.2_Missense_Mutation_p.R73M	NM_205849	NP_995321	Q8IZU0	FAM9B_HUMAN	family with sequence similarity 9, member B	28						nucleus					0		Hepatocellular(5;0.219)																---	---	---	---
WWC3	55841	broad.mit.edu	37	X	10084457	10084457	+	Splice_Site	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:10084457G>T	uc004csx.3	+	10	1173	c.975_splice	c.e10-1	p.R325_splice	WWC3_uc010nds.2_Splice_Site|WWC3_uc010ndt.2_Splice_Site	NM_015691	NP_056506			WWC family member 3											ovary(4)	4																		---	---	---	---
PRPS2	5634	broad.mit.edu	37	X	12838915	12838915	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12838915A>C	uc004cvb.2	+	6	981	c.857A>C	c.(856-858)AAG>ACG	p.K286T	PRPS2_uc004cva.2_Missense_Mutation_p.K289T|PRPS2_uc010nec.2_Missense_Mutation_p.K164T	NM_002765	NP_002756	P11908	PRPS2_HUMAN	phosphoribosyl pyrophosphate synthetase 2	286					nucleoside metabolic process|ribonucleoside monophosphate biosynthetic process		ATP binding|kinase activity|magnesium ion binding|protein homodimerization activity|ribose phosphate diphosphokinase activity				0																		---	---	---	---
GPM6B	2824	broad.mit.edu	37	X	13803833	13803833	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13803833G>A	uc004cvz.2	-	2	447	c.156C>T	c.(154-156)TGC>TGT	p.C52C	GPM6B_uc004cvx.2_Silent_p.C33C|GPM6B_uc011min.1_5'UTR|GPM6B_uc004cwa.2_Silent_p.C33C|GPM6B_uc004cvw.2_Silent_p.C92C|GPM6B_uc011mim.1_Silent_p.C66C|GPM6B_uc004cvy.2_Silent_p.C92C	NM_005278	NP_005269	Q13491	GPM6B_HUMAN	glycoprotein M6B isoform 3	52					cell differentiation|nervous system development	integral to membrane					0																		---	---	---	---
CNKSR2	22866	broad.mit.edu	37	X	21579685	21579685	+	Intron	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21579685G>A	uc004czx.1	+						CNKSR2_uc004czw.2_Intron|CNKSR2_uc011mjn.1_Intron|CNKSR2_uc011mjo.1_Intron|CNKSR2_uc004czy.2_Intron	NM_014927	NP_055742			connector enhancer of kinase suppressor of Ras						regulation of signal transduction	cytoplasm|membrane	protein binding			large_intestine(1)|lung(1)	2																		---	---	---	---
PDK3	5165	broad.mit.edu	37	X	24483644	24483644	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24483644G>A	uc004dbg.2	+	1	301	c.72G>A	c.(70-72)CCG>CCA	p.P24P	PDK3_uc004dbh.2_Silent_p.P24P	NM_005391	NP_005382	Q15120	PDK3_HUMAN	pyruvate dehydrogenase kinase 3 isoform 2	24					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	p.P24P(2)		lung(4)|upper_aerodigestive_tract(1)|ovary(1)	6																		---	---	---	---
POLA1	5422	broad.mit.edu	37	X	24807160	24807160	+	Intron	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24807160G>A	uc004dbl.2	+							NM_016937	NP_058633			DNA-directed DNA polymerase alpha 1						cell proliferation|DNA replication checkpoint|DNA replication, synthesis of RNA primer|DNA-dependent DNA replication initiation|double-strand break repair via nonhomologous end joining|interspecies interaction between organisms|lagging strand elongation|leading strand elongation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|cytoplasm|nuclear envelope|nuclear matrix|nucleolus|nucleoplasm	chromatin binding|DNA-directed DNA polymerase activity|metal ion binding|nucleoside binding			ovary(2)|skin(1)	3					Clofarabine(DB00631)|Fludarabine(DB01073)													---	---	---	---
GK	2710	broad.mit.edu	37	X	30714147	30714147	+	Intron	SNP	T	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30714147T>A	uc004dch.3	+						GK_uc010ngj.2_Intron|GK_uc004dci.3_Intron|GK_uc011mjz.1_Intron|GK_uc011mka.1_Intron|GK_uc010ngk.2_Intron	NM_203391	NP_976325			glycerol kinase isoform a						glycerol-3-phosphate metabolic process|triglyceride biosynthetic process	cytosol|mitochondrial outer membrane	ATP binding|glycerol kinase activity			central_nervous_system(1)	1																		---	---	---	---
FAM47B	170062	broad.mit.edu	37	X	34962701	34962701	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:34962701G>T	uc004ddi.1	+	1	1771	c.1753G>T	c.(1753-1755)GGT>TGT	p.G585C		NM_152631	NP_689844	Q8NA70	FA47B_HUMAN	hypothetical protein LOC170062	585										ovary(3)|breast(1)	4																		---	---	---	---
MED14	9282	broad.mit.edu	37	X	40552136	40552136	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40552136C>T	uc004dex.3	-	14	1809	c.1669G>A	c.(1669-1671)GTT>ATT	p.V557I		NM_004229	NP_004220	O60244	MED14_HUMAN	mediator complex subunit 14	557	Interaction with SREBF1.|Interaction with STAT2.				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	47662895	47662895	+	IGR	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47662895C>A								LOC100133957 (143119 upstream) : ZNF81 (33406 downstream)																																			---	---	---	---
SSX5	6758	broad.mit.edu	37	X	48054448	48054448	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48054448C>T	uc004dja.1	-						SSX5_uc004diz.1_Missense_Mutation_p.A63T	NM_175723	NP_783729			synovial sarcoma, X breakpoint 5 isoform b						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding				0																		---	---	---	---
HDAC6	10013	broad.mit.edu	37	X	48674000	48674000	+	Silent	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48674000C>A	uc011mmi.1	+	16	1370	c.1275C>A	c.(1273-1275)TCC>TCA	p.S425S	HDAC6_uc004dks.1_Silent_p.S425S|HDAC6_uc010nig.1_Silent_p.S273S|HDAC6_uc004dkt.1_Silent_p.S425S|HDAC6_uc011mmk.1_Silent_p.S406S|HDAC6_uc004dkv.1_Silent_p.S73S|HDAC6_uc004dkw.1_Silent_p.S73S	NM_006044	NP_006035	Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	425					aggresome assembly|cellular response to hydrogen peroxide|Hsp90 deacetylation|lysosome localization|macroautophagy|misfolded or incompletely synthesized protein catabolic process|negative regulation of proteolysis|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|polyubiquitinated misfolded protein transport|positive regulation of apoptosis|positive regulation of cellular chaperone-mediated protein complex assembly|positive regulation of epithelial cell migration|positive regulation of receptor biosynthetic process|positive regulation of signal transduction|regulation of androgen receptor signaling pathway|regulation of receptor activity|response to growth factor stimulus|response to toxin|transcription, DNA-dependent|tubulin deacetylation	aggresome|caveola|cell leading edge|cytosol|histone deacetylase complex|microtubule associated complex|perinuclear region of cytoplasm	actin binding|alpha-tubulin binding|beta-catenin binding|dynein complex binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|Hsp90 protein binding|microtubule binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|polyubiquitin binding|tau protein binding|tubulin deacetylase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)	4					Vorinostat(DB02546)													---	---	---	---
GRIPAP1	56850	broad.mit.edu	37	X	48846249	48846249	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48846249G>A	uc004dly.1	-	10	803	c.768C>T	c.(766-768)AGC>AGT	p.S256S	GRIPAP1_uc004dlz.2_Silent_p.S146S|GRIPAP1_uc004dma.2_Silent_p.S203S	NM_020137	NP_064522	Q4V328	GRAP1_HUMAN	GRIP1 associated protein 1 isoform 1	256	Potential.					early endosome				breast(2)|kidney(1)	3																		---	---	---	---
TFE3	7030	broad.mit.edu	37	X	48888035	48888035	+	Silent	SNP	C	T	T	rs1047561		TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48888035C>T	uc004dmb.3	-	10	1600	c.1362G>A	c.(1360-1362)TCG>TCA	p.S454S	TFE3_uc004dmc.3_Silent_p.S349S	NM_006521	NP_006512	P19532	TFE3_HUMAN	transcription factor E3	454					humoral immune response|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding		ASPSCR1/TFE3(161)|PRCC/TFE3(25)|SFPQ/TFE3(6)|NONO/TFE3(2)|CLTC/TFE3(2)	soft_tissue(120)|kidney(76)|central_nervous_system(1)	197								T	SFPQ|ASPSCR1|PRCC|NONO|CLTC	papillary renal|alveolar soft part sarcoma|renal								---	---	---	---
CLCN5	1184	broad.mit.edu	37	X	49856843	49856843	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49856843G>A	uc004dos.1	+	12	2456	c.2208G>A	c.(2206-2208)GCG>GCA	p.A736A	CLCN5_uc004dor.1_Silent_p.A806A|CLCN5_uc004doq.1_Silent_p.A806A|CLCN5_uc004dot.1_Silent_p.A736A	NM_000084	NP_000075	P51795	CLCN5_HUMAN	chloride channel 5 isoform b	736	CBS 2.|Cytoplasmic (By similarity).				excretion	apical part of cell|endosome membrane|Golgi membrane|integral to plasma membrane	antiporter activity|ATP binding			ovary(2)|lung(1)|central_nervous_system(1)	4	Ovarian(276;0.236)																	---	---	---	---
CCNB3	85417	broad.mit.edu	37	X	50051558	50051558	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50051558T>G	uc004dox.3	+	6	687	c.389T>G	c.(388-390)ATT>AGT	p.I130S	CCNB3_uc004doy.2_Missense_Mutation_p.I130S|CCNB3_uc004doz.2_Intron|CCNB3_uc010njq.2_Intron	NM_033031	NP_149020	Q8WWL7	CCNB3_HUMAN	cyclin B3 isoform 3	130					cell division|meiosis|regulation of cyclin-dependent protein kinase activity|regulation of G2/M transition of mitotic cell cycle	nucleus	protein kinase binding			ovary(4)|lung(3)|large_intestine(1)|pancreas(1)	9	Ovarian(276;0.236)																	---	---	---	---
TSPYL2	64061	broad.mit.edu	37	X	53112422	53112422	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53112422C>T	uc004drw.2	+	1	874	c.742C>T	c.(742-744)CGA>TGA	p.R248*	TSPYL2_uc004drv.2_Nonsense_Mutation_p.R248*|TSPYL2_uc004drx.1_5'Flank	NM_022117	NP_071400	Q9H2G4	TSYL2_HUMAN	TSPY-like 2	248					cell cycle|chromatin modification|negative regulation of cell cycle|negative regulation of cell growth|negative regulation of DNA replication|nucleosome assembly|regulation of protein kinase activity|regulation of signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	protein binding|rDNA binding				0																		---	---	---	---
KDM5C	8242	broad.mit.edu	37	X	53226954	53226954	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53226954T>G	uc004drz.2	-	18	3154	c.2621A>C	c.(2620-2622)AAG>ACG	p.K874T	KDM5C_uc011moc.1_RNA|KDM5C_uc011mod.1_Missense_Mutation_p.K807T|KDM5C_uc004dsa.2_Missense_Mutation_p.K873T	NM_004187	NP_004178	P41229	KDM5C_HUMAN	jumonji, AT rich interactive domain 1C isoform	874					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								---	---	---	---
USP51	158880	broad.mit.edu	37	X	55514020	55514020	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:55514020A>G	uc004dun.1	-	2	1432	c.1353T>C	c.(1351-1353)CAT>CAC	p.H451H	USP51_uc011moo.1_Silent_p.H155H	NM_201286	NP_958443	Q70EK9	UBP51_HUMAN	ubiquitin specific protease 51	451					ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3																		---	---	---	---
STARD8	9754	broad.mit.edu	37	X	67942294	67942294	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67942294A>G	uc004dxa.2	+	11	2737	c.2365A>G	c.(2365-2367)AGC>GGC	p.S789G	STARD8_uc004dxb.2_Missense_Mutation_p.S869G|STARD8_uc004dxc.3_Missense_Mutation_p.S789G	NM_014725	NP_055540	Q92502	STAR8_HUMAN	StAR-related lipid transfer (START) domain	789					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|focal adhesion	GTPase activator activity			breast(3)|ovary(2)|pancreas(1)	6																		---	---	---	---
AWAT1	158833	broad.mit.edu	37	X	69455926	69455926	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69455926G>A	uc004dxy.2	+	3	233	c.192G>A	c.(190-192)AGG>AGA	p.R64R		NM_001013579	NP_001013597	Q58HT5	AWAT1_HUMAN	wax synthase 1	64					lipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	long-chain-alcohol O-fatty-acyltransferase activity			ovary(3)	3																		---	---	---	---
KIF4A	24137	broad.mit.edu	37	X	69615683	69615683	+	Intron	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69615683A>G	uc004dyg.2	+						KIF4A_uc010nkw.2_Intron	NM_012310	NP_036442			kinesin family member 4						anterograde axon cargo transport|axon guidance|blood coagulation|organelle organization	chromosome|cytosol|midbody|nuclear matrix|spindle microtubule	ATP binding|DNA binding|microtubule motor activity|protein binding			ovary(4)	4																		---	---	---	---
NLGN3	54413	broad.mit.edu	37	X	70387433	70387433	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70387433C>T	uc004dzd.1	+	6	1686	c.1486C>T	c.(1486-1488)CGC>TGC	p.R496C	NLGN3_uc010nlb.1_Missense_Mutation_p.R456C|NLGN3_uc004dzb.2_Missense_Mutation_p.R476C|NLGN3_uc004dzc.2_Missense_Mutation_p.R359C|NLGN3_uc011mps.1_Missense_Mutation_p.R456C|NLGN3_uc004dze.2_Missense_Mutation_p.R294C	NM_018977	NP_061850	Q9NZ94	NLGN3_HUMAN	neuroligin 3	496	Extracellular (Potential).				neuron cell-cell adhesion|positive regulation of synaptogenesis|receptor-mediated endocytosis|social behavior|synapse assembly	cell surface|endocytic vesicle|integral to plasma membrane|synapse	neurexin binding|receptor activity			ovary(1)	1	Renal(35;0.156)																	---	---	---	---
NLGN3	54413	broad.mit.edu	37	X	70387487	70387487	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70387487A>G	uc004dzd.1	+	6	1740	c.1540A>G	c.(1540-1542)ATG>GTG	p.M514V	NLGN3_uc010nlb.1_Missense_Mutation_p.M474V|NLGN3_uc004dzb.2_Missense_Mutation_p.M494V|NLGN3_uc004dzc.2_Missense_Mutation_p.M377V|NLGN3_uc011mps.1_Missense_Mutation_p.M474V|NLGN3_uc004dze.2_Missense_Mutation_p.M312V	NM_018977	NP_061850	Q9NZ94	NLGN3_HUMAN	neuroligin 3	514	Extracellular (Potential).				neuron cell-cell adhesion|positive regulation of synaptogenesis|receptor-mediated endocytosis|social behavior|synapse assembly	cell surface|endocytic vesicle|integral to plasma membrane|synapse	neurexin binding|receptor activity			ovary(1)	1	Renal(35;0.156)																	---	---	---	---
OGT	8473	broad.mit.edu	37	X	70775226	70775226	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70775226G>A	uc004eaa.1	+	7	1132	c.915G>A	c.(913-915)GAG>GAA	p.E305E	BCYRN1_uc011mpt.1_Intron|OGT_uc004eab.1_Silent_p.E295E|OGT_uc004eac.2_Silent_p.E166E|OGT_uc004ead.2_Intron	NM_181672	NP_858058	O15294	OGT1_HUMAN	O-linked GlcNAc transferase isoform 1	305	TPR 8.				cellular response to retinoic acid|positive regulation of granulocyte differentiation|positive regulation of histone H3-K4 methylation|positive regulation of proteolysis|protein O-linked glycosylation|signal transduction	cytosol|MLL5-L complex	enzyme activator activity|protein binding|protein N-acetylglucosaminyltransferase activity			ovary(3)|kidney(1)|pancreas(1)	5	Renal(35;0.156)																	---	---	---	---
MAGEE2	139599	broad.mit.edu	37	X	75004692	75004692	+	Silent	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:75004692C>T	uc004ecj.1	-	1	380	c.195G>A	c.(193-195)CCG>CCA	p.P65P		NM_138703	NP_619648	Q8TD90	MAGE2_HUMAN	melanoma antigen family E, 2	65										ovary(1)|skin(1)	2																		---	---	---	---
ATRX	546	broad.mit.edu	37	X	76909629	76909629	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76909629G>A	uc004ecp.3	-	14	4508	c.4276C>T	c.(4276-4278)CGA>TGA	p.R1426*	ATRX_uc004ecq.3_Nonsense_Mutation_p.R1388*|ATRX_uc004eco.3_Nonsense_Mutation_p.R1211*|ATRX_uc004ecr.2_Nonsense_Mutation_p.R1358*	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1	1426					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						---	---	---	---
RPS6KA6	27330	broad.mit.edu	37	X	83419325	83419325	+	Intron	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83419325T>C	uc004eej.1	-						RPS6KA6_uc011mqt.1_Intron|RPS6KA6_uc011mqu.1_Intron	NM_014496	NP_055311			ribosomal protein S6 kinase polypeptide 6						axon guidance|central nervous system development|intracellular protein kinase cascade|synaptic transmission	cytosol|nucleoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(5)|stomach(1)|central_nervous_system(1)|skin(1)	8																		---	---	---	---
CPXCR1	53336	broad.mit.edu	37	X	88008465	88008465	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:88008465A>C	uc004efd.3	+	3	309	c.50A>C	c.(49-51)AAA>ACA	p.K17T	CPXCR1_uc004efc.3_Missense_Mutation_p.K17T	NM_033048	NP_149037	Q8N123	CPXCR_HUMAN	CPX chromosome region, candidate 1	17						intracellular	zinc ion binding			ovary(3)	3																		---	---	---	---
TSPAN6	7105	broad.mit.edu	37	X	99891634	99891634	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99891634C>T	uc004ega.1	-	1	161	c.58G>A	c.(58-60)GTT>ATT	p.V20I	TSPAN6_uc010nna.1_5'UTR	NM_003270	NP_003261	O43657	TSN6_HUMAN	transmembrane 4 superfamily member 6	20	Helical; (Potential).				positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane	signal transducer activity			ovary(1)	1																		---	---	---	---
CSTF2	1478	broad.mit.edu	37	X	100088417	100088417	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100088417A>G	uc004egh.2	+	11	1514	c.1456A>G	c.(1456-1458)AGT>GGT	p.S486G	CSTF2_uc010nnd.2_Missense_Mutation_p.S506G|CSTF2_uc004egi.2_Missense_Mutation_p.S469G	NM_001325	NP_001316	P33240	CSTF2_HUMAN	cleavage stimulation factor subunit 2	486	Gly/Pro-rich.				mRNA cleavage|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	cleavage body|mRNA cleavage and polyadenylation specificity factor complex	nucleotide binding|protein binding|protein binding|RNA binding			skin(1)	1																		---	---	---	---
CENPI	2491	broad.mit.edu	37	X	100375746	100375746	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100375746A>G	uc004egx.2	+	7	930	c.660A>G	c.(658-660)AGA>AGG	p.R220R	CENPI_uc011mrg.1_Silent_p.R220R|CENPI_uc004egy.2_Silent_p.R220R	NM_006733	NP_006724	Q92674	CENPI_HUMAN	centromere protein I	220					CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	cytosol|kinetochore|nucleoplasm	protein binding			skin(1)	1																		---	---	---	---
NXF3	56000	broad.mit.edu	37	X	102338321	102338321	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102338321C>T	uc004eju.2	-						NXF3_uc010noi.1_Intron|NXF3_uc011mrw.1_Intron|NXF3_uc011mrx.1_Intron	NM_022052	NP_071335			nuclear RNA export factor 3							cytoplasm|nuclear RNA export factor complex	nucleocytoplasmic transporter activity|nucleotide binding|protein binding			ovary(1)|lung(1)|central_nervous_system(1)	3																		---	---	---	---
TCEAL5	340543	broad.mit.edu	37	X	102529243	102529243	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102529243C>A	uc004ejz.1	-	3	544	c.249G>T	c.(247-249)AAG>AAT	p.K83N		NM_001012979	NP_001012997	Q5H9L2	TCAL5_HUMAN	transcription elongation factor A (SII)-like 5	83					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(1)|breast(1)	2																		---	---	---	---
RAB40A	142684	broad.mit.edu	37	X	102755489	102755489	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102755489T>C	uc004ekk.2	-	3	538	c.196A>G	c.(196-198)AAG>GAG	p.K66E		NM_080879	NP_543155	Q8WXH6	RB40A_HUMAN	RAB40A, member RAS oncogene family	66					protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding				0																		---	---	---	---
PLP1	5354	broad.mit.edu	37	X	103041663	103041663	+	Intron	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:103041663T>C	uc010nov.2	+						RAB9B_uc004eli.1_Intron|PLP1_uc004elk.2_Intron|PLP1_uc004elj.2_Intron|PLP1_uc011msf.1_Intron|PLP1_uc010now.1_Missense_Mutation_p.I158T|PLP1_uc010nox.2_Intron	NM_001128834	NP_001122306			proteolipid protein 1 isoform 1						cell death|synaptic transmission	integral to membrane				ovary(1)	1																		---	---	---	---
TEX13A	56157	broad.mit.edu	37	X	104464772	104464772	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:104464772C>T	uc004ema.2	-	2	422	c.310G>A	c.(310-312)GCA>ACA	p.A104T	IL1RAPL2_uc004elz.1_Intron|TEX13A_uc004emb.2_Missense_Mutation_p.A104T	NM_031274	NP_112564	Q9BXU3	TX13A_HUMAN	testis expressed sequence 13A	104						intracellular	zinc ion binding			ovary(2)	2																		---	---	---	---
MUM1L1	139221	broad.mit.edu	37	X	105449828	105449828	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105449828C>T	uc004emf.1	+	4	1052	c.403C>T	c.(403-405)CGG>TGG	p.R135W	MUM1L1_uc004emg.1_Missense_Mutation_p.R135W	NM_152423	NP_689636	Q5H9M0	MUML1_HUMAN	melanoma associated antigen (mutated) 1-like 1	135										ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
CXorf57	55086	broad.mit.edu	37	X	105879841	105879841	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105879841C>T	uc004emi.3	+	7	1523	c.1372C>T	c.(1372-1374)CTC>TTC	p.L458F	CXorf57_uc004emj.3_Missense_Mutation_p.L458F|CXorf57_uc004emh.2_Missense_Mutation_p.L458F	NM_018015	NP_060485	Q6NSI4	CX057_HUMAN	hypothetical protein LOC55086	458										ovary(1)|lung(1)|breast(1)	3																		---	---	---	---
TBC1D8B	54885	broad.mit.edu	37	X	106065338	106065338	+	Silent	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106065338A>G	uc004emo.2	+	4	657	c.492A>G	c.(490-492)TCA>TCG	p.S164S	MORC4_uc004emp.3_Intron|TBC1D8B_uc004emm.2_Silent_p.S164S|TBC1D8B_uc004emn.2_Silent_p.S164S	NM_017752	NP_060222	Q0IIM8	TBC8B_HUMAN	TBC1 domain family, member 8B (with GRAM domain)	164	GRAM 1.					intracellular	calcium ion binding|Rab GTPase activator activity			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
MORC4	79710	broad.mit.edu	37	X	106224218	106224218	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106224218C>T	uc004emu.3	-	7	1082	c.839G>A	c.(838-840)CGC>CAC	p.R280H	MORC4_uc004emp.3_Intron|MORC4_uc004emv.3_Missense_Mutation_p.R280H|MORC4_uc004emw.3_Missense_Mutation_p.R28H	NM_024657	NP_078933	Q8TE76	MORC4_HUMAN	zinc finger, CW type with coiled-coil domain 2	280							ATP binding|zinc ion binding			ovary(1)	1																		---	---	---	---
COL4A6	1288	broad.mit.edu	37	X	107406175	107406175	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107406175C>T	uc004enw.3	-	41	4269	c.4166G>A	c.(4165-4167)GGC>GAC	p.G1389D	COL4A6_uc004env.3_Missense_Mutation_p.G1388D|COL4A6_uc011msn.1_Missense_Mutation_p.G1364D|COL4A6_uc010npk.2_Missense_Mutation_p.G1331D|COL4A6_uc011msm.1_5'Flank|COL4A6_uc010npj.2_5'UTR	NM_001847	NP_001838	Q14031	CO4A6_HUMAN	type IV alpha 6 collagen isoform A precursor	1389	Triple-helical region.				cell adhesion|extracellular matrix organization	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(6)|urinary_tract(1)|large_intestine(1)	8														Alport_syndrome_with_Diffuse_Leiomyomatosis				---	---	---	---
COL4A5	1287	broad.mit.edu	37	X	107939595	107939595	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107939595T>C	uc004enz.1	+	52	5265	c.5063T>C	c.(5062-5064)ATG>ACG	p.M1688T	COL4A5_uc011mso.1_Missense_Mutation_p.M1685T|COL4A5_uc011msp.1_Missense_Mutation_p.M364T	NM_033380	NP_203699	P29400	CO4A5_HUMAN	type IV collagen alpha 5 isoform 2 precursor	1682	Collagen IV NC1.		Missing (in APSX).|Missing (in APSX).		axon guidance	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(3)|central_nervous_system(1)	4														Alport_syndrome_with_Diffuse_Leiomyomatosis				---	---	---	---
IRS4	8471	broad.mit.edu	37	X	107979319	107979319	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107979319G>A	uc004eoc.2	-	1	289	c.256C>T	c.(256-258)CGG>TGG	p.R86W		NM_003604	NP_003595	O14654	IRS4_HUMAN	insulin receptor substrate 4	86	PH.					plasma membrane	insulin receptor binding|SH3/SH2 adaptor activity|signal transducer activity			ovary(4)|large_intestine(2)|lung(1)|breast(1)|skin(1)|pancreas(1)	10																		---	---	---	---
ACSL4	2182	broad.mit.edu	37	X	108926137	108926137	+	Intron	SNP	A	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:108926137A>C	uc004eoi.2	-						ACSL4_uc004eoj.2_Intron|ACSL4_uc004eok.2_Intron|ACSL4_uc010npp.1_Intron	NM_022977	NP_075266			acyl-CoA synthetase long-chain family member 4						fatty acid metabolic process|learning or memory|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane	ATP binding|long-chain fatty acid-CoA ligase activity			large_intestine(1)|lung(1)|ovary(1)	3					Icosapent(DB00159)|Troglitazone(DB00197)													---	---	---	---
TRPC5	7224	broad.mit.edu	37	X	111019716	111019716	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:111019716C>T	uc004epl.1	-	11	3666	c.2747G>A	c.(2746-2748)AGT>AAT	p.S916N		NM_012471	NP_036603	Q9UL62	TRPC5_HUMAN	transient receptor potential cation channel,	916	Cytoplasmic (Potential).				axon guidance	calcium channel complex|integral to plasma membrane	protein binding|store-operated calcium channel activity			urinary_tract(1)	1																		---	---	---	---
ZCCHC12	170261	broad.mit.edu	37	X	117959632	117959632	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117959632G>T	uc004equ.2	+	4	898	c.425G>T	c.(424-426)GGG>GTG	p.G142V		NM_173798	NP_776159	Q6PEW1	ZCH12_HUMAN	zinc finger, CCHC domain containing 12	142					regulation of transcription, DNA-dependent|transcription, DNA-dependent		nucleic acid binding|zinc ion binding			ovary(1)	1																		---	---	---	---
CUL4B	8450	broad.mit.edu	37	X	119675494	119675494	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119675494A>G	uc004esw.2	-	12	1897	c.1460T>C	c.(1459-1461)GTT>GCT	p.V487A	CUL4B_uc010nqq.2_Missense_Mutation_p.V186A|CUL4B_uc004esv.2_Missense_Mutation_p.V469A	NM_003588	NP_003579	Q13620	CUL4B_HUMAN	cullin 4B isoform 1	487					cell cycle|DNA repair|ubiquitin-dependent protein catabolic process	Cul4B-RING ubiquitin ligase complex|nucleus	protein binding|ubiquitin protein ligase binding			lung(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
CUL4B	8450	broad.mit.edu	37	X	119694483	119694483	+	Intron	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119694483G>A	uc004esw.2	-						CUL4B_uc004esv.2_Missense_Mutation_p.T4I	NM_003588	NP_003579			cullin 4B isoform 1						cell cycle|DNA repair|ubiquitin-dependent protein catabolic process	Cul4B-RING ubiquitin ligase complex|nucleus	protein binding|ubiquitin protein ligase binding			lung(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
ODZ1	10178	broad.mit.edu	37	X	123631020	123631020	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123631020C>A	uc004euj.2	-	20	3605	c.3541G>T	c.(3541-3543)GCC>TCC	p.A1181S	ODZ1_uc011muj.1_Missense_Mutation_p.A1180S|ODZ1_uc010nqy.2_Missense_Mutation_p.A1181S	NM_014253	NP_055068	Q9UKZ4	TEN1_HUMAN	odz, odd Oz/ten-m homolog 1 isoform 3	1181	Extracellular (Potential).				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																		---	---	---	---
DCAF12L2	340578	broad.mit.edu	37	X	125299339	125299339	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:125299339C>T	uc004euk.1	-	1	596	c.569G>A	c.(568-570)CGC>CAC	p.R190H		NM_001013628	NP_001013650	Q5VW00	DC122_HUMAN	DDB1 and CUL4 associated factor 12-like 2	190										lung(2)|skin(2)|large_intestine(1)|pancreas(1)|ovary(1)	7																		---	---	---	---
MBNL3	55796	broad.mit.edu	37	X	131573522	131573522	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:131573522G>T	uc004ewv.3	-	1	197	c.118C>A	c.(118-120)CCA>ACA	p.P40T	MBNL3_uc004eww.2_5'UTR|MBNL3_uc010nrl.1_RNA|MBNL3_uc004ewu.3_Missense_Mutation_p.P40T	NM_018388	NP_060858	Q9NUK0	MBNL3_HUMAN	muscleblind-like 3 isoform G	40	C3H1-type 1.				mRNA processing|multicellular organismal development|regulation of RNA splicing|RNA splicing	Golgi apparatus|nucleus	nucleic acid binding|zinc ion binding				0	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
MAP7D3	79649	broad.mit.edu	37	X	135328232	135328232	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135328232T>G	uc004ezt.2	-	3	336	c.245A>C	c.(244-246)CAG>CCG	p.Q82P	MAP7D3_uc004ezs.2_Missense_Mutation_p.Q81P|MAP7D3_uc011mwc.1_Missense_Mutation_p.Q64P|MAP7D3_uc010nsa.1_Missense_Mutation_p.Q81P	NM_024597	NP_078873	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	82	Potential.					cytoplasm|spindle				ovary(2)|central_nervous_system(1)|skin(1)	4	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
RBMX	27316	broad.mit.edu	37	X	135957412	135957412	+	Intron	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135957412C>T	uc004fae.1	-						RBMX_uc004fac.1_5'Flank|RBMX_uc011mwf.1_Intron|RBMX_uc004fad.1_Intron|RBMX_uc011mwg.1_Intron|RBMX_uc004faf.1_Intron|RBMX_uc010nsf.1_Intron|RBMX_uc004fag.1_Intron	NM_002139	NP_002130			RNA binding motif protein, X-linked isoform 1							catalytic step 2 spliceosome|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
GPR101	83550	broad.mit.edu	37	X	136113015	136113015	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:136113015C>A	uc011mwh.1	-	1	819	c.819G>T	c.(817-819)AAG>AAT	p.K273N		NM_054021	NP_473362	Q96P66	GP101_HUMAN	G protein-coupled receptor 101	273	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)|lung(1)|skin(1)	5	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
ZIC3	7547	broad.mit.edu	37	X	136649449	136649449	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:136649449G>A	uc004fak.2	+	1	1104	c.599G>A	c.(598-600)CGC>CAC	p.R200H		NM_003413	NP_003404	O60481	ZIC3_HUMAN	zinc finger protein of the cerebellum 3	200					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)																	---	---	---	---
SLITRK2	84631	broad.mit.edu	37	X	144905145	144905145	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:144905145T>C	uc004fcd.2	+	5	2192	c.1202T>C	c.(1201-1203)TTG>TCG	p.L401S	SLITRK2_uc010nsp.2_Missense_Mutation_p.L401S|SLITRK2_uc010nso.2_Missense_Mutation_p.L401S|SLITRK2_uc011mwq.1_Missense_Mutation_p.L401S|SLITRK2_uc011mwr.1_Missense_Mutation_p.L401S|SLITRK2_uc011mws.1_Missense_Mutation_p.L401S|SLITRK2_uc004fcg.2_Missense_Mutation_p.L401S|SLITRK2_uc011mwt.1_Missense_Mutation_p.L401S	NM_032539	NP_115928	Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2 precursor	401	Extracellular (Potential).|LRR 8.					integral to membrane				ovary(5)|central_nervous_system(1)|pancreas(1)	7	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
CXorf1	9142	broad.mit.edu	37	X	144909226	144909226	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:144909226T>C	uc004fch.2	+	1	299	c.31T>C	c.(31-33)TCA>CCA	p.S11P		NM_004709	NP_004700	O96002	CX001_HUMAN	hypothetical protein LOC9142	11											0	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
IDS	3423	broad.mit.edu	37	X	148564330	148564330	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:148564330T>C	uc011mxe.1	-	9	1798	c.1600A>G	c.(1600-1602)AAT>GAT	p.N534D	IDS_uc011mxd.1_Missense_Mutation_p.N137D|IDS_uc011mxf.1_Missense_Mutation_p.N444D|IDS_uc011mxg.1_Missense_Mutation_p.N323D|IDS_uc010nsu.1_Missense_Mutation_p.N144D|IDS_uc004fcw.3_Missense_Mutation_p.N323D	NM_000202	NP_000193	P22304	IDS_HUMAN	iduronate-2-sulfatase isoform a precursor	534						lysosome	iduronate-2-sulfatase activity|metal ion binding				0	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)																	---	---	---	---
GPR50	9248	broad.mit.edu	37	X	150348483	150348483	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150348483G>A	uc010ntg.1	+	2	563	c.428G>A	c.(427-429)CGC>CAC	p.R143H	uc004fes.1_5'Flank|GPR50_uc011myc.1_Missense_Mutation_p.R143H	NM_004224	NP_004215	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	143	Cytoplasmic (Potential).				cell-cell signaling	integral to plasma membrane	melatonin receptor activity			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
MAGEA12	4111	broad.mit.edu	37	X	151899845	151899845	+	3'UTR	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151899845C>A	uc010ntp.2	-	3					MAGEA12_uc004fgb.2_Intron|MAGEA12_uc004fgc.2_3'UTR	NM_005367	NP_005358			melanoma antigen family A, 12											skin(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
CSAG1	158511	broad.mit.edu	37	X	151908890	151908890	+	Silent	SNP	C	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151908890C>A	uc004fge.2	+	4	457	c.129C>A	c.(127-129)TCC>TCA	p.S43S	CSAG1_uc004fgf.2_Silent_p.S43S|CSAG1_uc004fgd.2_RNA	NM_153478	NP_705611	Q6PB30	CSAG1_HUMAN	chondrosarcoma associated gene 1 precursor	43										ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
HCFC1	3054	broad.mit.edu	37	X	153222107	153222107	+	Silent	SNP	G	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153222107G>T	uc004fjp.2	-	15	3132	c.2604C>A	c.(2602-2604)GCC>GCA	p.A868A		NM_005334	NP_005325	P51610	HCFC1_HUMAN	host cell factor 1	868	Interaction with ZBTB17.|Interaction with GABP2.				cell cycle|interspecies interaction between organisms|positive regulation of cell cycle|positive regulation of gene expression|protein stabilization|reactivation of latent virus|regulation of protein complex assembly|transcription from RNA polymerase II promoter	mitochondrion|MLL1 complex|MLL5-L complex|Set1C/COMPASS complex	chromatin binding|identical protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)	2	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
HCFC1	3054	broad.mit.edu	37	X	153225576	153225576	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153225576C>T	uc004fjp.2	-	8	1649	c.1121G>A	c.(1120-1122)CGC>CAC	p.R374H		NM_005334	NP_005325	P51610	HCFC1_HUMAN	host cell factor 1	374					cell cycle|interspecies interaction between organisms|positive regulation of cell cycle|positive regulation of gene expression|protein stabilization|reactivation of latent virus|regulation of protein complex assembly|transcription from RNA polymerase II promoter	mitochondrion|MLL1 complex|MLL5-L complex|Set1C/COMPASS complex	chromatin binding|identical protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)	2	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
IRAK1	3654	broad.mit.edu	37	X	153278578	153278578	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153278578T>C	uc004fjs.1	-	12	1925	c.1846A>G	c.(1846-1848)AGG>GGG	p.R616G	IRAK1_uc004fjr.1_Missense_Mutation_p.R586G|IRAK1_uc004fjt.1_Missense_Mutation_p.R537G|IRAK1_uc010nur.2_Intron	NM_001569	NP_001560	P51617	IRAK1_HUMAN	interleukin-1 receptor-associated kinase 1	616					activation of MAPK activity|activation of NF-kappaB-inducing kinase activity|anti-apoptosis|innate immune response|interleukin-1-mediated signaling pathway|JNK cascade|lipopolysaccharide-mediated signaling pathway|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of NF-kappaB transcription factor activity|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|protein autophosphorylation|protein oligomerization|regulation of cytokine-mediated signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transmembrane receptor protein serine/threonine kinase signaling pathway	cytosol|endosome membrane|interleukin-1 receptor complex	ATP binding|NF-kappaB-inducing kinase activity|protein binding|protein heterodimerization activity|protein homodimerization activity|ubiquitin-protein ligase activity			lung(5)|ovary(2)|breast(1)|central_nervous_system(1)	9	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)																	---	---	---	---
CTAG2	30848	broad.mit.edu	37	X	153880794	153880794	+	Silent	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153880794G>A	uc004fmi.1	-	2	434	c.381C>T	c.(379-381)ACC>ACT	p.T127T	CTAG2_uc004fmh.1_Silent_p.T127T	NM_020994	NP_066274	O75638	CTAG2_HUMAN	cancer/testis antigen 2 isoform LAGE-1b	127						centrosome				pancreas(1)	1	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)																	---	---	---	---
F8	2157	broad.mit.edu	37	X	154157267	154157267	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154157267T>C	uc004fmt.2	-	14	4969	c.4798A>G	c.(4798-4800)AAA>GAA	p.K1600E		NM_000132	NP_000123	P00451	FA8_HUMAN	coagulation factor VIII isoform a precursor	1600	B.				acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation	extracellular space|plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity|protein binding			ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	11	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)													---	---	---	---
TMLHE	55217	broad.mit.edu	37	X	154741394	154741394	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154741394G>A	uc004fnn.2	-	5	864	c.698C>T	c.(697-699)GCG>GTG	p.A233V	TMLHE_uc004fno.2_Missense_Mutation_p.A233V|TMLHE_uc004fnp.3_Missense_Mutation_p.A233V	NM_018196	NP_060666	Q9NVH6	TMLH_HUMAN	trimethyllysine hydroxylase, epsilon	233					carnitine biosynthetic process	mitochondrial matrix	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|trimethyllysine dioxygenase activity			ovary(1)	1	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)				Succinic acid(DB00139)|Vitamin C(DB00126)													---	---	---	---
SPRY3	10251	broad.mit.edu	37	X	155004380	155004380	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4190-01A-01D-1126-08	TCGA-BR-4190-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:155004380G>A	uc004fnq.1	+	2	1301	c.847G>A	c.(847-849)GCC>ACC	p.A283T	SPRY3_uc010nvl.1_Missense_Mutation_p.A184T	NM_005840	NP_005831	O43610	SPY3_HUMAN	sprouty homolog 3	283					multicellular organismal development|regulation of signal transduction	cytoplasm|membrane					0	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)																	---	---	---	---
